===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-77- --lt-dump-script)
sift-4.0.3b/bin/seqs_to_matrixweb:78: lt_dump_D=`$ECHO "X$lt_script_arg0" | /usr/local/bin/sed -e 's/^X//' -e 's%/[^/]*$%%'`
sift-4.0.3b/bin/seqs_to_matrixweb-79- test "X$lt_dump_D" = "X$lt_script_arg0" && lt_dump_D=.
sift-4.0.3b/bin/seqs_to_matrixweb:80: lt_dump_F=`$ECHO "X$lt_script_arg0" | /usr/local/bin/sed -e 's/^X//' -e 's%^.*/%%'`
sift-4.0.3b/bin/seqs_to_matrixweb-81- cat "$lt_dump_D/$lt_dump_F"
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-104- $ECHO "seqs_to_matrixweb:seqs_to_matrixweb:${LINENO}: newargv[$lt_dump_args_N]: $lt_arg"
sift-4.0.3b/bin/seqs_to_matrixweb:105: lt_dump_args_N=`expr $lt_dump_args_N + 1`
sift-4.0.3b/bin/seqs_to_matrixweb-106- done
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-142- # Find the directory that this script lives in.
sift-4.0.3b/bin/seqs_to_matrixweb:143: thisdir=`$ECHO "$file" | /usr/local/bin/sed 's%/[^/]*$%%'`
sift-4.0.3b/bin/seqs_to_matrixweb-144- test "x$thisdir" = "x$file" && thisdir=.
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-146- # Follow symbolic links until we get to the real thisdir.
sift-4.0.3b/bin/seqs_to_matrixweb:147: file=`ls -ld "$file" | /usr/local/bin/sed -n 's/.*-> //p'`
sift-4.0.3b/bin/seqs_to_matrixweb-148- while test -n "$file"; do
sift-4.0.3b/bin/seqs_to_matrixweb:149: destdir=`$ECHO "$file" | /usr/local/bin/sed 's%/[^/]*$%%'`
sift-4.0.3b/bin/seqs_to_matrixweb-150-
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-158-
sift-4.0.3b/bin/seqs_to_matrixweb:159: file=`$ECHO "$file" | /usr/local/bin/sed 's%^.*/%%'`
sift-4.0.3b/bin/seqs_to_matrixweb:160: file=`ls -ld "$thisdir/$file" | /usr/local/bin/sed -n 's/.*-> //p'`
sift-4.0.3b/bin/seqs_to_matrixweb-161- done
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-172- case "$thisdir" in
sift-4.0.3b/bin/seqs_to_matrixweb:173: *[\\/].libs ) thisdir=`$ECHO "$thisdir" | /usr/local/bin/sed 's%[\\/][^\\/]*$%%'` ;;
sift-4.0.3b/bin/seqs_to_matrixweb-174- .libs ) thisdir=. ;;
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-178- # Try to get the absolute directory name.
sift-4.0.3b/bin/seqs_to_matrixweb:179: absdir=`cd "$thisdir" && pwd`
sift-4.0.3b/bin/seqs_to_matrixweb-180- test -n "$absdir" && thisdir="$absdir"
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-185- if test ! -f "$progdir/$program" ||
sift-4.0.3b/bin/seqs_to_matrixweb:186: { file=`ls -1dt "$progdir/$program" "$progdir/../$program" 2>/dev/null | /usr/local/bin/sed 1q`; \
sift-4.0.3b/bin/seqs_to_matrixweb-187- test "X$file" != "X$progdir/$program"; }; then
##############################################
sift-4.0.3b/bin/seqs_to_matrixweb-198- if test -n "$relink_command"; then
sift-4.0.3b/bin/seqs_to_matrixweb:199: if relink_command_output=`eval $relink_command 2>&1`; then :
sift-4.0.3b/bin/seqs_to_matrixweb-200- else
##############################################
sift-4.0.3b/bin/SIFT_subroutines.pm-15- $file = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/bin/SIFT_subroutines.pm:16: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/bin/SIFT_subroutines.pm-17-if ($status ==0) {
##############################################
sift-4.0.3b/bin/SIFT_subroutines.pm-26- $file = $tmp . "/$pid" . ".siftresults.matrix";
sift-4.0.3b/bin/SIFT_subroutines.pm:27: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/bin/SIFT_subroutines.pm-28-
sift-4.0.3b/bin/SIFT_subroutines.pm-29-#send predictions
sift-4.0.3b/bin/SIFT_subroutines.pm:30: @table_files = `ls $tmp/$pid.aatable*`;
sift-4.0.3b/bin/SIFT_subroutines.pm-31- $index = 0;
##############################################
sift-4.0.3b/bin/SIFT_subroutines.pm-41- $index++;
sift-4.0.3b/bin/SIFT_subroutines.pm:42: system("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/bin/SIFT_subroutines.pm-43- }
sift-4.0.3b/bin/SIFT_subroutines.pm-44-# mail any errors
sift-4.0.3b/bin/SIFT_subroutines.pm:45: @error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/bin/SIFT_subroutines.pm-46- for $file (@error_files) {
##############################################
sift-4.0.3b/bin/SIFT_subroutines.pm-48- $tempstring = "\"$subject\""; $subject = $tempstring;
sift-4.0.3b/bin/SIFT_subroutines.pm:49: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/bin/SIFT_subroutines.pm-50- }
##############################################
sift-4.0.3b/bin/SIFT_subroutines.pm-121-# START
sift-4.0.3b/bin/SIFT_subroutines.pm:122:#$no_pic_files = `ls $tmp/$$.*.ps | wc -l`;
sift-4.0.3b/bin/SIFT_subroutines.pm-123-#print_logos_desc($no_pic_files, $$);
##############################################
sift-4.0.3b/bin/DNA_PROT_SUBROUTINES.pl-337-
sift-4.0.3b/bin/DNA_PROT_SUBROUTINES.pl:338: my $seqtmp = `zcat $gz_chr_file | head -2 | tail -1`;
sift-4.0.3b/bin/DNA_PROT_SUBROUTINES.pl-339- $_ = $seqtmp;
##############################################
sift-4.0.3b/bin/DNA_PROT_SUBROUTINES.pl-352-
sift-4.0.3b/bin/DNA_PROT_SUBROUTINES.pl:353: my @seq = `zcat $gz_chr_file | head -$linestart | tail -$numlines`;
sift-4.0.3b/bin/DNA_PROT_SUBROUTINES.pl-354- my $basestart = $start_pos % $linewidth;
##############################################
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl-125- close (CHR_FILE_NEW);
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl:126: system("mv $all_chr_file.new $all_chr_file");
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl-127-}
##############################################
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl-166-if ($job_size == 0){
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl:167: system("rm -f $tmp/$new_pid.chrfile");
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl-168- print OUTPAGE "Complete set\t";
##############################################
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl-197-close (OUTPAGE);
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl:198:#system("cp $tmp/$pid.outpage.txt $tmp/$pid.outpage.swap.txt");
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl-199-#direct to the outpage url
##############################################
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl-213-}
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl:214:system("$bin/sift_feed_to_chr_coords_batch.pl $tmp/$pid.batchfile $tmp $Variation_db_dir");
sift-4.0.3b/bin/SIFT_exome_nssnvs.pl-215-close (BATCH_FILE);
##############################################
sift-4.0.3b/bin/SIFT_exome_indels.pl-72-#check input validity and reformat chrfile
sift-4.0.3b/bin/SIFT_exome_indels.pl:73:system("perl $reformat_chrfile $all_chr_file $tmp");
sift-4.0.3b/bin/SIFT_exome_indels.pl-74-
##############################################
sift-4.0.3b/bin/SIFT_exome_indels.pl-80-#convert chrfile to gff for intersecting with small indel errors file.
sift-4.0.3b/bin/SIFT_exome_indels.pl:81:system("perl $indelfile_to_gff $all_chr_file");
sift-4.0.3b/bin/SIFT_exome_indels.pl-82-$all_chr_gff_file = "$all_chr_file.gff";
##############################################
sift-4.0.3b/bin/SIFT_exome_indels.pl-84-#Now intersect gff chrfile with small indels ref file
sift-4.0.3b/bin/SIFT_exome_indels.pl:85:system("$intersect_locations $all_chr_gff_file gff $small_indels_error_gff gff simple > $small_indels_error_intersect_file");
sift-4.0.3b/bin/SIFT_exome_indels.pl-86-
##############################################
sift-4.0.3b/bin/SIFT_exome_indels.pl-102-#Creat binned SNP files for SNP Classifier
sift-4.0.3b/bin/SIFT_exome_indels.pl:103:system("$bin/map_coords_to_bin_indels.pl $bin_file $all_chr_file $pid $tmp");
sift-4.0.3b/bin/SIFT_exome_indels.pl-104-#create index of old coords to new coords using pid_old_new_coords_map.txt
##############################################
sift-4.0.3b/bin/SIFT_exome_indels.pl-257- my $modified_seq = $elts[6];
sift-4.0.3b/bin/SIFT_exome_indels.pl:258: @indel_location_features = split /\t/, `$model_transcript $enst $indel_start $indel_stop $Variation_db_dir`;
sift-4.0.3b/bin/SIFT_exome_indels.pl-259- $indel_start_CDS = $indel_location_features[0];
##############################################
sift-4.0.3b/bin/SIFT_exome_indels.pl-277- $outfile = "$tmp/$pid\_$enst\_$hit_id\_comparison.fasta";
sift-4.0.3b/bin/SIFT_exome_indels.pl:278: @indel_result = split /\t/, `$detect_indel $original_seq $modified_seq $outfile`;
sift-4.0.3b/bin/SIFT_exome_indels.pl-279- $aa_coords_original = $indel_result[0];
##############################################
sift-4.0.3b/bin/SIFT_exome_indels.pl-307-my $repeat_detect_output_file = "$tmp/$pid\_repeat_detect_output_file.txt";
sift-4.0.3b/bin/SIFT_exome_indels.pl:308:system("$detect_repeat $repeat_detect_input_file $repeat_db_file > $repeat_detect_output_file");
sift-4.0.3b/bin/SIFT_exome_indels.pl-309-
##############################################
sift-4.0.3b/bin/SIFT_exome_indels.pl-806- # lockfile will wait until it can lock the file
sift-4.0.3b/bin/SIFT_exome_indels.pl:807: `./lockfile $lockqueuefile`;
sift-4.0.3b/bin/SIFT_exome_indels.pl-808-
##############################################
sift-4.0.3b/bin/Classify_SNPs_Indels.pl-821- my $stmpfile = "tmp008";
sift-4.0.3b/bin/Classify_SNPs_Indels.pl:822: system ("echo \">query\n$query_seq\n\" > $qtmpfile");
sift-4.0.3b/bin/Classify_SNPs_Indels.pl:823: system ("echo \">subject\n$subject_seq\n\" > $stmpfile");
sift-4.0.3b/bin/Classify_SNPs_Indels.pl:824: my $result = `blast -p blastp -i $qtmpfile -j $stmpfile`; # | grep Identities | head -n 1`;
sift-4.0.3b/bin/Classify_SNPs_Indels.pl-825-
##############################################
sift-4.0.3b/bin/SIFT_intersect_cds.pl-88-
sift-4.0.3b/bin/SIFT_intersect_cds.pl:89: system ("sort -k1,1 -k4,4n -k5,5n $new_chr_file > $new_chr_file.sorted");
sift-4.0.3b/bin/SIFT_intersect_cds.pl:90:my @lines_to_get = `$bin/IntersectLocations.sh $new_chr_file.sorted gff $coding_file gff simple | grep -v Total | cut -f1 | uniq`;
sift-4.0.3b/bin/SIFT_intersect_cds.pl-91-
##############################################
sift-4.0.3b/bin/indelfile_to_gff.pl-33-close (GFFFILE);
sift-4.0.3b/bin/indelfile_to_gff.pl:34:system ("sort -k1,1 -k4,4n -k5,5n $snpfile.journal > $snpfile.gff");
sift-4.0.3b/bin/indelfile_to_gff.pl-35-unlink("$snpfile.journal");
##############################################
sift-4.0.3b/bin/reformat_chrfile.pl-69-}
sift-4.0.3b/bin/reformat_chrfile.pl:70:system ("mv $tempfile $chrfile");
##############################################
sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl-27-
sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl:28: system ("$bin/snv_db_engine.pl $tmp $Variation_db_dir $master_pid $pid $chrfile $org $seq_identity_filter $last_partition $COORD_SYSTEM $output_options $address");
sift-4.0.3b/bin/sift_feed_to_chr_coords_batch.pl-29-}
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-74-#Creat binned SNP files for querying human chr database- the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/bin/snv_db_engine.pl:75:system("$bin/map_coords_to_bin.pl $bin_file $all_chr_file $pid $tmp");
sift-4.0.3b/bin/snv_db_engine.pl-76-
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-88- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/bin/snv_db_engine.pl:89: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/bin/snv_db_engine.pl-90- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-119- #}
sift-4.0.3b/bin/snv_db_engine.pl:120: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/bin/snv_db_engine.pl-121- ###
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-127- ### uncomment following block if using in operator - see above
sift-4.0.3b/bin/snv_db_engine.pl:128: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/bin/snv_db_engine.pl:129: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/bin/snv_db_engine.pl-130- $sth_db_chr->execute();
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-134- }
sift-4.0.3b/bin/snv_db_engine.pl:135: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/bin/snv_db_engine.pl-136- ###
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-236- $row2 = "$row\t$ensg\t$gene_name\t$gene_desc\t$ensfm\t$fam_desc\t$gene_status\t$fam_size\t$kaks_mouse\t$kaks_macaque\t$mim_status\t$freq_av\t$freq_ceu";
sift-4.0.3b/bin/snv_db_engine.pl:237: #system("echo $row2 >> $tmp/remove1");
sift-4.0.3b/bin/snv_db_engine.pl-238- $key = "$chr\t$coord1\t$coord2\t$CDS\t$ensp_exists";
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-335- #print "$row<BR>";
sift-4.0.3b/bin/snv_db_engine.pl:336: #system("echo $row >> $tmp/remove");
sift-4.0.3b/bin/snv_db_engine.pl-337- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-580-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/bin/snv_db_engine.pl:581:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/bin/snv_db_engine.pl-582-
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-689- close (OUTPAGE);
sift-4.0.3b/bin/snv_db_engine.pl:690: system ("chmod 755 $tmp/$master_pid.outpage.modified.txt");
sift-4.0.3b/bin/snv_db_engine.pl-691- rename "$tmp/$master_pid.outpage.modified.txt", "$tmp/$master_pid.outpage.txt"
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-733- close (OUTPAGE);
sift-4.0.3b/bin/snv_db_engine.pl:734: system ("chmod 755 $tmp/$master_pid.outpage.modified.txt");
sift-4.0.3b/bin/snv_db_engine.pl-735- rename "$tmp/$master_pid.outpage.modified.txt", "$tmp/$master_pid.outpage.txt"
##############################################
sift-4.0.3b/bin/snv_db_engine.pl-1024- # lockfile will wait until it can lock the file
sift-4.0.3b/bin/snv_db_engine.pl:1025: `./lockfile $lockqueuefile`;
sift-4.0.3b/bin/snv_db_engine.pl-1026-
##############################################
sift-4.0.3b/web/scripts/get_BLINK_grid_seq_batch_ALL.sh-6-# to this software.
sift-4.0.3b/web/scripts/get_BLINK_grid_seq_batch_ALL.sh:7:for pid in `cat $1`
sift-4.0.3b/web/scripts/get_BLINK_grid_seq_batch_ALL.sh-8-do
##############################################
sift-4.0.3b/web/scripts/get_median_aln.pl-60- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_median_aln.pl:61: system("/usr/local/projects/SIFT/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh $q_loc $a_loc $s_loc $pid $outdir_partition");
sift-4.0.3b/web/scripts/get_median_aln.pl-62- }
##############################################
sift-4.0.3b/web/scripts/get_median_aln.pl-72- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_median_aln.pl:73: system("/usr/local/projects/SIFT/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh $q_loc $a_loc $s_loc $pid $outdir_partition");
sift-4.0.3b/web/scripts/get_median_aln.pl-74- }
##############################################
sift-4.0.3b/web/scripts/separate_queries.sh-6-# to this software.
sift-4.0.3b/web/scripts/separate_queries.sh:7:for batch in `cat $1`
sift-4.0.3b/web/scripts/separate_queries.sh-8-do
##############################################
sift-4.0.3b/web/scripts/separate_queries.sh-13- do
sift-4.0.3b/web/scripts/separate_queries.sh:14: pid=`echo $file |sed s/\.alignedfasta//`
sift-4.0.3b/web/scripts/separate_queries.sh-15- /usr/local/projects/GOSII/pkumar/tmp/scripts/get_first_seq.pl $file > query/$pid.seq
##############################################
sift-4.0.3b/web/scripts/get_BLINK_seq_batch_BEST.sh-6-# to this software.
sift-4.0.3b/web/scripts/get_BLINK_seq_batch_BEST.sh:7:for pid in `cat $1`
sift-4.0.3b/web/scripts/get_BLINK_seq_batch_BEST.sh-8-do
##############################################
sift-4.0.3b/web/scripts/rename.sh-6-# to this software.
sift-4.0.3b/web/scripts/rename.sh:7:for part in `cat $1`
sift-4.0.3b/web/scripts/rename.sh-8-do
##############################################
sift-4.0.3b/web/scripts/rename.sh-11- mkdir renamed
sift-4.0.3b/web/scripts/rename.sh:12: for file in `cat list`; do pid=`head -n 2 $file | grep ">" | awk -F\| '{print $4}'`;cp $file renamed/$pid.alignedfasta; done
sift-4.0.3b/web/scripts/rename.sh-13- rm list;
##############################################
sift-4.0.3b/web/scripts/get_median_aln_grid.pl-61- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_median_aln_grid.pl:62: system("qsub -P 08010 -j y -V -cwd -l \"arch=lx*64\" /usr/local/projects/SIFT/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh $q_loc $a_loc $s_loc $pid $outdir_partition");
sift-4.0.3b/web/scripts/get_median_aln_grid.pl-63- }
##############################################
sift-4.0.3b/web/scripts/get_median_aln_grid.pl-75- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_median_aln_grid.pl:76: system("qsub -P 08010 -j y -V -cwd -l \"arch=lx*64\" /usr/local/projects/SIFT/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh $q_loc $a_loc $s_loc $pid $outdir_partition");
sift-4.0.3b/web/scripts/get_median_aln_grid.pl-77- }
##############################################
sift-4.0.3b/web/scripts/get_BLINK_seq_batch.sh-6-# to this software.
sift-4.0.3b/web/scripts/get_BLINK_seq_batch.sh:7:for pid in `cat $1`
sift-4.0.3b/web/scripts/get_BLINK_seq_batch.sh-8-do
##############################################
sift-4.0.3b/web/scripts/submitMuscle_batch_partition.sh-8-inDir=`pwd`/$inDir_name
sift-4.0.3b/web/scripts/submitMuscle_batch_partition.sh:9:outDir_name=`echo $1 | sed s/partition/aligned/`
sift-4.0.3b/web/scripts/submitMuscle_batch_partition.sh-10-outDir=`pwd`/$outDir_name
sift-4.0.3b/web/scripts/submitMuscle_batch_partition.sh-11-mkdir $outDir
sift-4.0.3b/web/scripts/submitMuscle_batch_partition.sh:12:for file in `ls $1`
sift-4.0.3b/web/scripts/submitMuscle_batch_partition.sh-13-do
##############################################
sift-4.0.3b/web/scripts/get_median_aln_errored.pl-61- print "$pid\n";
sift-4.0.3b/web/scripts/get_median_aln_errored.pl:62: system("/usr/local/projects/GOSII/pkumar/tmp/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh $q_loc $a_loc s_loc $pid $e_loc_new");
sift-4.0.3b/web/scripts/get_median_aln_errored.pl-63-}
##############################################
sift-4.0.3b/web/scripts/get_sift_prediction_errored.pl-60- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_sift_prediction_errored.pl:61: system("/usr/local/projects/GOSII/pkumar/tmp/scripts/from_sift/SIFT_prediction.csh $q_loc $s_loc $e_loc_new $pid >& $e_loc/prediction.log");
sift-4.0.3b/web/scripts/get_sift_prediction_errored.pl-62- print "$pid\t$e_loc\n";
##############################################
sift-4.0.3b/web/scripts/submitMuscle_batch.sh-6-# to this software.
sift-4.0.3b/web/scripts/submitMuscle_batch.sh:7:for partition in `cat $1`
sift-4.0.3b/web/scripts/submitMuscle_batch.sh-8-do
##############################################
sift-4.0.3b/web/scripts/muscle.sh-9-inFile=$1
sift-4.0.3b/web/scripts/muscle.sh:10:inFile_name=`echo $inFile | awk -F\/ '{print $NF}'`
sift-4.0.3b/web/scripts/muscle.sh-11-outFile_name=$inFile_name.aln.out
##############################################
sift-4.0.3b/web/scripts/index_query.sh-6-# to this software.
sift-4.0.3b/web/scripts/index_query.sh:7:for batch in `cat $1`
sift-4.0.3b/web/scripts/index_query.sh-8-do
sift-4.0.3b/web/scripts/index_query.sh-9- cd $batch/renamed/query
sift-4.0.3b/web/scripts/index_query.sh:10: for file in `ls *.seq`; do pid=`echo $file | sed s/.seq//`;path=`pwd`;echo -e $pid "\t" $path; done >> ../../../../query_location_$2.txt
sift-4.0.3b/web/scripts/index_query.sh-11- cd ../../../
##############################################
sift-4.0.3b/web/scripts/index_alignments.sh-6-# to this software.
sift-4.0.3b/web/scripts/index_alignments.sh:7:for batch in `cat $1`
sift-4.0.3b/web/scripts/index_alignments.sh-8-do
sift-4.0.3b/web/scripts/index_alignments.sh-9- cd $batch/renamed
sift-4.0.3b/web/scripts/index_alignments.sh:10: for file in `ls *.alignedfasta`; do pid=`echo $file | sed s/.alignedfasta//`;path=`pwd`;echo -e $pid "\t" $path; done >> ../../../aln_locations_$2.txt
sift-4.0.3b/web/scripts/index_alignments.sh-11- cd ../../
##############################################
sift-4.0.3b/web/scripts/index_prediction.sh-6-# to this software.
sift-4.0.3b/web/scripts/index_prediction.sh:7:for batch in `cat $1`
sift-4.0.3b/web/scripts/index_prediction.sh-8-do
##############################################
sift-4.0.3b/web/scripts/index_prediction.sh-12- do
sift-4.0.3b/web/scripts/index_prediction.sh:13: pid=`echo $result | awk -F_result '{print $1}'`
sift-4.0.3b/web/scripts/index_prediction.sh:14: file=`ls $result/*.prediction`
sift-4.0.3b/web/scripts/index_prediction.sh-15- path=`pwd`
##############################################
sift-4.0.3b/web/scripts/get_median_aln_grid_fast.pl-93- #print "COMMAND: $command\n";
sift-4.0.3b/web/scripts/get_median_aln_grid_fast.pl:94: system("$command");
sift-4.0.3b/web/scripts/get_median_aln_grid_fast.pl-95-
##############################################
sift-4.0.3b/web/scripts/get_median_aln_grid_fast.pl-107-$command = "qsub -P 08010 -j y -V -cwd -l \"arch=lx*64\" /usr/local/projects/SIFT/scripts/from_sift/seqs_chosen_via_median_info_from_list.pl $out";
sift-4.0.3b/web/scripts/get_median_aln_grid_fast.pl:108:system("$command");
##############################################
sift-4.0.3b/web/scripts/get_median_aln_errored_grid.pl-61- print "$pid\n";
sift-4.0.3b/web/scripts/get_median_aln_errored_grid.pl:62: system("qsub -P 08010 -j y -V -cwd -o $e_loc_new -l \"arch=lx*64\" /usr/local/projects/GOSII/pkumar/tmp/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh $q_loc $a_loc s_loc $pid $e_loc_new");
sift-4.0.3b/web/scripts/get_median_aln_errored_grid.pl-63-}
##############################################
sift-4.0.3b/web/scripts/from_sift/seqs_chosen_via_median_info_from_list.pl-7-while (<FILE>){
sift-4.0.3b/web/scripts/from_sift/seqs_chosen_via_median_info_from_list.pl:8: system("/usr/local/projects/SIFT/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh $_");
sift-4.0.3b/web/scripts/from_sift/seqs_chosen_via_median_info_from_list.pl-9-}
##############################################
sift-4.0.3b/web/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh-39-set alignedseqs = $tmpdir/$pid.alignedfasta
sift-4.0.3b/web/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh:40:set fileSize=`stat -c %s $tmpdir/$pid.selected`
sift-4.0.3b/web/scripts/from_sift/seqs_chosen_via_median_info_pkumar.csh-41-
##############################################
sift-4.0.3b/web/scripts/get_sift_prediction.pl-60- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_sift_prediction.pl:61: system("/usr/local/projects/GOSII/pkumar/tmp/scripts/from_sift/SIFT_prediction.csh $q_loc $s_loc $outdir_partition $pid >& $resultdir/prediction.log");
sift-4.0.3b/web/scripts/get_sift_prediction.pl-62- print "$pid\t$resultdir\n";
##############################################
sift-4.0.3b/web/scripts/get_sift_prediction.pl-69- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_sift_prediction.pl:70: system("/usr/local/projects/GOSII/pkumar/tmp/scripts/from_sift/SIFT_prediction.csh $q_loc $s_loc $outdir_partition $pid >& $resultdir/prediction.log");
sift-4.0.3b/web/scripts/get_sift_prediction.pl-71- print "$pid\t$resultdir\n";
##############################################
sift-4.0.3b/web/scripts/get_sift_prediction_grid.pl-60- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_sift_prediction_grid.pl:61: system("qsub -P 08010 -j y -V -cwd -o $resultdir -l \"arch=lx*64\" /usr/local/projects/GOSII/pkumar/tmp/scripts/from_sift/SIFT_prediction.csh $q_loc $s_loc $outdir_partition $pid");
sift-4.0.3b/web/scripts/get_sift_prediction_grid.pl-62- }
##############################################
sift-4.0.3b/web/scripts/get_sift_prediction_grid.pl-68- $s_loc = $s_index{$pid};
sift-4.0.3b/web/scripts/get_sift_prediction_grid.pl:69: system("qsub -P 08010 -j y -V -cwd -o $resultdir -l \"arch=lx*64\" /usr/local/projects/GOSII/pkumar/tmp/scripts/from_sift/SIFT_prediction.csh $q_loc $s_loc $outdir_partition $pid");
sift-4.0.3b/web/scripts/get_sift_prediction_grid.pl-70- }
##############################################
sift-4.0.3b/web/scripts/get_BLINK_seq_batch_ALL.sh-6-# to this software.
sift-4.0.3b/web/scripts/get_BLINK_seq_batch_ALL.sh:7:for pid in `cat $1`
sift-4.0.3b/web/scripts/get_BLINK_seq_batch_ALL.sh-8-do
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_pseudogene.pdf-44-m"&?X?#Om+m"IjF-F#SV.)i?`].LDR5^6aHpTh55G[oE^[AN,(dhaNEW)U)/fXP8*
sift-4.0.3b/web/www/SIFT_on_databases/Figure_pseudogene.pdf:45:,m,XG,9WnbT6<u`%9Uq$eAXcsX5!1GjsufbB5V##+0+"DlcPB:XMEk91J3q5`S[ni
sift-4.0.3b/web/www/SIFT_on_databases/Figure_pseudogene.pdf-46-IJ[&oJ_:,>8_VftG9qWb>^`d;pF@Lo]4c"dD#6<CB%m)Gj]/qP\.(m!T^O!OKjDb<
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-26-<^h.p4epM/+-"Bq-4u=7l]9pfHS'HT=tc?PP]d4`I2LD-'tDM/bDZ]W(")mZZ`4#R
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:27::LtUCnbcJAE`Vt*oXLa2;n\b!@2$+X<f`eJYg_olYYd&!;F/Yp]d?Iek39GL\su.P
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-28-[nc8Jp7I1Bp.t"8cfQO<bnL*WP>7K-,WGi1@PM"I]1"JD8[kZLJ%L$&'si1jaIFS7
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-50-^g9-Pl:jDJe_lH1-I8/*8#2!q=?LUhcUEA5C>Aqb^:0])E[G9S(QZ70GrAU\:Qs'W
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:51:`9$kpr!^cQc,JdWJBDAPb)66g#@YhUH'C]ki5XdH"%&%L6B;/A%`D&77hLn>b?R/Y
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-52-?g'4OkV5?PJX@VQ#cBFmF)e*!9Dkd0!#5\)#_5UN7p%0L2A_]CDRH(T'E]82!U:?8
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-58->[A0cSVU^@VtqHq"612&?5?dP(*&m$@@*n'Zc?M6f)S^8GK)&Gi92"9E]8F`lcB?d
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:59:C#7D/]6W7MOBhI!Q[<Hl?g8/3$fj!g`[Do`RP-qDf)7$5*u1h*@>O+6q`!p:qrMqm
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-60-mcj?3^F\"+5J>REC1&d3idu%74NMZ>=@&=_X$)Ng9A%>Q2n!c&HG]7?/PmU5/k*!r
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:61:Ybn.)H`i$]gp:061Kc[i75r?4'IsGVP0tXMOI6/$g70LX=VIkZ$q]/o-1"`GG-FE5
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-62-KOl&jZ%=YT.:9ppR5oeCcj%ZM8e\9K$q]/o-1"H?D*M69-CL<3"^sdHaH\G3e#3PM
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-138-e`k>ZPnZQ@O*m".DdJj#i^0C%]S_X_b0jh_*kO2kFU_0Ek)F*%XJ?C_c-1<d$%psu
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:139:dF`$EGT@YPPYErT/Rk%NlfLR7$#LTf.k-,_1Zf_l#*%G]<m,m\-8AOLRqCed`%DL&
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-140-]k_Q.I.;)#Kb._5hIFEq[<qE"/d?0%XACh"bdE65K?PV>nYnVm5Q1,FA$"Ff(W.T/
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-180-/ME<SIJPsi9c!<-KmjOda!cH1\E.;-fr)St=u\%nCCC%W"+5dmqHlC'H'rLBduR#"
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:181:Rk3bB$iM";*9I%#*j`LQ:A3r$kC1/YXs(`1aDc8I^3Udi!nlKF:R+u*$MiBW5=HF7
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-182-ZLk=A\%GBmqt,(P]'`Y<%>8s4@rD]]4U-1_SDYd/T9"A+aO_4(4i@AbZ1(hU>@&YG
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-208-IL5MH8H7u*VjX(AduT+sc3jC$6@Zf;>_hsT?@AEeAj?6(1gE!njD,-N\0LZ;e(3pD
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:209:^%sjTbs)*WET+R'D_1NB%+.HAq!MI:R`WZ8rDI@gXH9V;n6:Kl6a$IWe`W?:p?BU"
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-210-+4RrrD_1P>&Q5'&s4s_O1HF,a^Q!gQkCn;#JUbUWUa0kBGHX3VA@#)3*)q/KhcT)$
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-221-IJF\>>0eGQ#!tGi4<ER\oCU1@+=Hs&YBdV?Km[a25L**Ug@&'f:LoYBI?+-9OKKkE
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:222:HTEZngHpC9jY`1B^$shHN5H%_7RFf+FV3]3oCU1@+t#DH#C[8`?Q?incOc8Pd%=Wi
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-223-%q3@"psUnR5///2(ttBe_TtN#+(naur.P2Hj0SFOq2KhDs8VT[^OQ4Vp[P$Tp=n1@
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-242-D(gL#MVq:FI/EhfHr=lqDtm'1ph=&Ml_3CqqYL+Z^Q&8Cq"`g^rqlTf;18?/l]:kt
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:243:59JN0i"XT9&N\.")<Ub`T.ntZY/5KlTAP\o5N0C2=EJ5$oVgdU,O?eo$`-mqf%8B&
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-244-d(=Ebe*B.m`?h!TSB-MR9IdBh?db'2^3LHQ(3/NqKpJY`eD\sIZmkXZ-Rg^2:;2,0
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-245-2kNUW22!sU5VZi,h`VHpJSah08,-306GBn*?WrKDT07(;R;DT]pOP-[o=/`G+[0j\
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:246:QhG/c`f$U%0=kH!AmS#0d_oqM(Z!p-P`s2L?MN<^GZhP@5jrsP<>XKZ8]j]%P:o-/
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-247-=u@ho)f,:(k%=#,*j`LQ:A3qik8bAabOVK`IXlL:]'a`;>$`PHIJL;2_Kd;3>LW%U
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-255-o!L@RVK]`0j-H%RAtOP=&Jra9nseM/7YHUi?$a+1/ME=5^AL<1.pg<Kf(AX:GIP*C
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:256:-*kXZSjGVO=h:3t7^BAWmRbPmjN`)A9!i22#hRMSc)eC$SFR<GjO8l_D`M?2^7"X`
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-257-L3Z?tH?W.g?7(0Q$hT`LO+_9SnH.a6^@(D1LV,l1pqgO7<O5$+[\g55]t;6009JuC
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-309-;'h[3Z.GF`;t@b_Rf8aYAW0V=4/UM\UJ2'SfFB9VM(1mBB1u:O>=3nn;skoUD3K=_
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:310:6`A$]CF*aLfN?GW?/`abm-0[5c8%,h@nXAC+P\bHaQ`0pQ@AVr_CaK3aUFhI8T@Xe
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-311-(;Ik]aVU=Tnq8J[\2N+jD:"[Fr)aB?PU;-NjD*'N*8roWN0K*V=Y"c0rLYHSi:mag
##############################################
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-340-hC$"9R@u4p4,:R%giD/J>HF84b[Qp3UP\1>hk+[Xr?cm13ikD,#qKp5.I#n8dH"pd
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf:341:]SDqL`ij2"#$,[RM80Qfd;7;HpI,>G"eihZc`3)_X?b_TFrp0b@s*S];QsJB"PD55
sift-4.0.3b/web/www/SIFT_on_databases/Figure_redundantmotif.pdf-342-Ppf0L+JlMV*Xdc?3_he;"]fJ#TPle/oK8k>J7nFkI\sXW7'gk/KDUka]Fb[Cp0Q[G
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl-189- close (CHR_FILE_NEW);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl:190: system("mv $all_chr_file.new $all_chr_file");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl-191-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl-231-if ($job_size == 0){
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl:232: system("rm -f $tmp/$new_pid.chrfile");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl-233- $outpage_content .= "<tr class=\"tableRow".($outpage_counter++ % 2 == 0 ? 'Even' : 'Odd')."\"><td><p>Complete set</p></td>";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl-285-close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl:286:#system("cp $tmp/$pid.outpage.html $tmp/$pid.outpage.swap.html");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl-287-#direct to the outpage url
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl-301-}
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl:302:system("$bin/SIFT_feed_to_chr_coords_batch.pl $tmp/$pid.batchfile");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords.pl-303-close (BATCH_FILE);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-51-#Creat binned SNP files for querying human chr database- the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:52:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-53-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-65- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:66: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-67- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-96- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:97: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-98- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-103- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:104: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:105: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-106- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-110- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:111: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-112- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-213- $row2 = "$row\t$ensg\t$gene_name\t$gene_desc\t$ensfm\t$fam_desc\t$gene_status\t$fam_size\t$kaks_mouse\t$kaks_macaque\t$mim_status\t$freq_av\t$freq_ceu";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:214: #system("echo $row2 >> $tmp/remove1");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-215- $key = "$chr\t$coord1\t$coord2\t$CDS\t$ensp_exists";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-333- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:334: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-335- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-553-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:554:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-555-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-557- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:558:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-559- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-648-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:649:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-650-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-811- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:812: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-813- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-855- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:856: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-857- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-1146- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl:1147: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_020510.pl-1148-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-52-#Creat binned SNP files for querying human chr database- the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:53:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-54-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-66- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:67: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-68- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-90- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:91: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-92- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-97- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:98: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:99: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-100- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-104- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:105: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-106- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-142- push @ {$index_query_result{$key}}, $row;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:143: #system("echo $row >> $tmp/$pid.remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-144-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-234- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:235: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-236- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-386-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:387:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-388-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-390- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:391:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-392- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-529-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:530:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-531-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-680- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:681: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-682- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-724- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:725: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-726- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-921- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl:922: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_old.pl-923-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-90-if ($address ne "") {
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl:91: system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-92- print "IP address " . $ENV{REMOTE_ADDR}. " <BR>";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-95- # Put it in the SIFT2 (not SIFT) queue
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl:96: system("./add_queue_entry.pl SIFT2_queue $program_call $pid NCBI_blink $names{gi_number} $out 0 $subst_file 0 $seq_identity_filter $sequences_to_select $address > $comments 2> /dev/null");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-97- exit(0);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-109-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl:110: system("$program_call $pid NCBI_blink $names{gi_number} $out 0 $subst_file 0 $seq_identity_filter $sequences_to_select $address > $comments 2>&1");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-111-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-116-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl:117:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-118-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-136-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl:137:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-138-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-156-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl:157:system ("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-158-#errors or warnings that don't disrupt program
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-171-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl:172:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-173-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-178- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl:179: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_PNtest.pl-180- print "<A HREF=\"/pauline-bin/catfile.csh?btest-tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl-168-
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl:169: #system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl-170-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl-598- my $all_hits_alignment_file =
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl:599:`ls /home/sift/BLink_alignments/Predictions_ALL_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl-600-
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl-601- my $best_hits_alignment_file =
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl:602:`ls /home/sift/BLink_alignments/Predictions_BEST_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl-603- chomp($all_hits_alignment_file);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl-608- my $newfile2 = "/home/sift/tmp/" . $protein . ".besthits.msf";
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl:609: system("cp $all_hits_alignment_file $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl:610: system("cp $best_hits_alignment_file $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl:611: system("chmod 660 $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl:612: system("chmod 660 $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_dbsnp_submit.pl-613-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-118- #NOTE: Results are actually mailed by $program_call
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:119: system("./add_queue_entry.pl SIFT_queue $program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2> /dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-120-#query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-124-{
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:125:# system ("./add_queue_entry.pl SIFT_queue $program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2> /dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:126: system("$program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2>&1");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:127: system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-128-# Pauline commented out background &");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-134-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:135:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-136-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-153-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:154:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-155-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-171-print "<BR>\n";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:172:system ("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-173-#errors or warnings that don't disrupt program
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-186-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:187:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-188-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-198- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl:199: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_121307.pl-200- print "<A HREF=\"/pauline-bin/catfile.csh?btest-tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-112-#check input validity and reformat chrfile
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:113:system("perl $reformat_chrfile $all_chr_file");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-114-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-123-#convert chrfile to gff for intersecting with small indel errors file.
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:124:system("perl $indelfile_to_gff $all_chr_file");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-125-$all_chr_gff_file = "$all_chr_file.gff";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-127-#Now intersect gff chrfile with small indels ref file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:128:system("$intersect_locations $all_chr_gff_file gff $small_indels_error_gff gff simple > $small_indels_error_intersect_file");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-129-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-145-#Creat binned SNP files for SNP Classifier
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:146:system("$bin/map_coords_to_bin_indels.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-147-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-301- my $modified_seq = $elts[6];
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:302: @indel_location_features = split /\t/, `$model_transcript $enst $indel_start $indel_stop`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-303- $indel_start_CDS = $indel_location_features[0];
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-321- $outfile = "$tmp/$pid\_$enst\_$hit_id\_comparison.fasta";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:322: @indel_result = split /\t/, `$detect_indel $original_seq $modified_seq $outfile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-323- $aa_coords_original = $indel_result[0];
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-351-my $repeat_detect_output_file = "$tmp/$pid\_repeat_detect_output_file.txt";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:352:system("$detect_repeat $repeat_detect_input_file > $repeat_detect_output_file");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-353-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-376-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:377:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-378-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-380- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:381:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-382- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-949- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl:950: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit.pl-951-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-119-#Creat binned SNP files for SNP Classifier
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl:120:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-121-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-305-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl:306:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-307-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-309- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl:310:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-311- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-387- $alignedfasta = "$tmp\/$pid\.$gi.alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl:388: system("cp $address_aln_best $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-389- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-412- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl:413: system("cp $address_aln_all $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-414- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-432- $psiblastout = $alignedfasta;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl:433: $seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-434- $seqno--; # subtract the QUERY sequence
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-435-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl:436: system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-437-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-862- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl:863: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_refseq.pl-864-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_batch.pl-29- close(OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_batch.pl:30: system ("$bin/SIFT_chr_coords_submit.pl $master_pid $pid $chrfile $org $seq_identity_filter $last_partition $COORD_SYSTEM $output_options $address");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_batch.pl-31-}
##############################################
sift-4.0.3b/web/sift-bin/protomat.csh-59-
sift-4.0.3b/web/sift-bin/protomat.csh:60:set minlen = (`grep " MINIMUM" $name.motifj.pros | awk '{print $2}'`)
sift-4.0.3b/web/sift-bin/protomat.csh-61-if ($minlen < 8) then
##############################################
sift-4.0.3b/web/sift-bin/protomat.csh-65- # Model heuristic; needs MINIMUM sequence length from $name.motifj.pros
sift-4.0.3b/web/sift-bin/protomat.csh:66: set model = (`$bindir/model.run $name.motifj.pros`)
sift-4.0.3b/web/sift-bin/protomat.csh-67- $bindir/gibbs $name.motifj.pros $model -f -s3 >& $name.gblks
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-39-#mkdir $tmp;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:40:#system("chmod 777 * -R $tmp");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-41-my $all_chr_file = @ARGV[2];
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-53-#Creat binned SNP files for SNP Classifier - the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:54:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-55-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-66- #$time = join(":", @timeData[2,1,0]) ;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:67: #system("echo connecting to Human_CHR$chr.sqlite $time >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-68- $db_chr =DBI->connect( "dbi:SQLite:dbname=/opt/www/sift/db/Human_db/Human_CHR$chr.sqlite","", "", { RaiseError => 1, AutoCommit => 1 } );
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-70- #$time = join(":", @timeData[2,1,0]) ;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:71: #system("echo connected to Human_CHR$chr.sqlite $time >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-72- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-92- #$time = join(":", @timeData[2,1,0]);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:93: #system("echo compiling prep statement $table_chr where chr = chr$chr started $time >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-94-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:95: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-96- #@timeData = localtime(time);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-97- #$time = join(":", @timeData[2,1,0]) ;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:98: #system("echo compiling prep statement $table_chr where chr = chr$chr finished $time >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:99: #system("echo select * from $table_chr where chr = chr$chr AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str) >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:100: #print "select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-101- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-103- #$time = join(":", @timeData[2,1,0]);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:104: #system("echo query executed $time >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-105-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-112-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:113: #system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-114-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-137- push @ {$index_query_result{$key}}, $row;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:138: #system("echo $row >> $tmp/$pid.remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-139-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-222- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:223: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-224- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-391-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:392:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-393-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-395- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:396:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-397- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-456- $address_aln_enst = "$datadir\/" . @rows_enst_address[0];
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:457: system("cp $address_aln_enst $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-458- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-476- );
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:477: system("rm -f $tmp/$pid.$enst.substfile ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:478: system("rm -f $alignedfasta $alignedfasta.2 $alignedfasta.gapsremoved");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:479: system("rm -f $tmp/$pid.$enst.siftresults.matrix");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:480: system("rm -f $tmp/$pid.$enst.comments");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-481-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-485- #$psiblastout = $alignedfasta;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:486: #$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-487- #$seqno--; # subtract the QUERY sequence
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-488-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:489: #system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-490-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-720-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:721:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-722-if ($last_partition == 1){
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-723- for ($i = $master_pid + 1; $i <= $pid; $i ++){
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:724: system("cat $tmp/$i.combined_siftresults.predictions.table.html >> $tmp/$master_pid.combined_siftresults.predictions.table.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:725: system("cat $tmp/$i.combined_siftresults.predictions.tsv >> $tmp/$master_pid.combined_siftresults.predictions.tsv");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-726- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-793- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:794: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-795- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-990- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl:991: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_db_without_score.pl-992-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-104- $program_call = $bin . "/SIFT.start.csh";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:105: exec ("$program_call $pid query_seq $queryseqfile $out 27 $subst_file $gap_option $seq_identity_filter $names{database} $address > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-106- exit;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-110- $file = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:111: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-112- print "mail $subject $return_address $address $file ";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-120-$program_call = $bin . "/SIFTING.csh";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:121:system("$program_call $pid query_seq $queryseqfile $out 27 $subst_file $gap_option $seq_identity_filter $names{database} > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:122:@error_files = `ls $tmp/$$.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-123-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-133- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:134: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-135- print "<A HREF=\"/sift-bin/catfile.csh?$tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-137- }
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:138:# system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-139- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-146-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:147:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-148-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-163-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:164:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-165-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-210-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:211:system ("rm -f $tmp/$$.comments*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:212:system ("rm -f $tmp/$$.tmp");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-213-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:214:#system ("rm -f $tmp/$$*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl:215:#system ("rm -f $tmp/*$$");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit.pl-216-
##############################################
sift-4.0.3b/web/sift-bin/reformat_chrfile.pl-67-}
sift-4.0.3b/web/sift-bin/reformat_chrfile.pl:68:system ("mv $tempfile $chrfile");
##############################################
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl-108-
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl:109:system("/howard/servers/btest/bin/fastaseqs $query $queryclean");
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl:110:system ("/howard/servers/btest/bin/fastaseqs $dbase $dbaseclean");
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl-111-
##############################################
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl-113-
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl:114:#system("$bin/PHAT_submission.csh $queryclean $txmem $dbaseclean $nontxmem_matrix $txmem_matrix > $out 2>&1");
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl-115-
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl:116:system("$bin/PHAT_submission.csh $queryclean $txmem $dbaseclean $nontxmem_matrix $txmem_matrix > $out 2>/dev/null");
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl-117-
##############################################
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl-126-
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl:127:system ("rm $out");
sift-4.0.3b/web/sift-bin/PHAT_submission_backup.pl-128-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-39-#mkdir $tmp;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:40:#system("chmod 777 * -R $tmp");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-41-my $all_chr_file = @ARGV[2];
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-53-#Creat binned SNP files for SNP Classifier - the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:54:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-55-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-82- ### comment this block if using in operator see below.
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:83: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 = ?");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-84- #$sth_db_chr->execute("$coord2");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-88- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:89: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-90- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-95- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:96: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-97- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-101- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:102: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-103- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-127- push @ {$index_query_result{$key}}, $row;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:128: #system("echo $row >> $tmp/$pid.remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-129-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-218- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:219: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-220- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-370-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:371:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-372-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-374- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:375:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-376- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-501-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:502:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-503-if ($last_partition == 1){
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-504- for ($i = $master_pid + 1; $i <= $pid; $i ++){
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:505: system("cat $tmp/$i.combined_siftresults.predictions.table.html >> $tmp/$master_pid.combined_siftresults.predictions.table.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:506: system("cat $tmp/$i.combined_siftresults.predictions.tsv >> $tmp/$master_pid.combined_siftresults.predictions.tsv");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-507- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-574- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:575: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-576- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-771- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl:772: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_in_operator.pl-773-
##############################################
sift-4.0.3b/web/sift-bin/format.pl-43-#>>>>Generates message in Apache error_log if none of these
sift-4.0.3b/web/sift-bin/format.pl:44:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/format.pl-45-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/format.pl-56- print "<BR>";
sift-4.0.3b/web/sift-bin/format.pl:57: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/format.pl-58- print "<A HREF=\"/sift-bin/catfile.csh?$tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/format.pl-60- }
sift-4.0.3b/web/sift-bin/format.pl:61:#>>> system ("rm -f $tmp/$pid.*"); <<<<NO!
sift-4.0.3b/web/sift-bin/format.pl-62- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/format.pl-69-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/format.pl:70:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/format.pl-71-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/format.pl-84-
sift-4.0.3b/web/sift-bin/format.pl:85:$no_table_files = `ls $tmp/$pid.aatable* |grep -v html | wc -l`;
sift-4.0.3b/web/sift-bin/format.pl-86-
##############################################
sift-4.0.3b/web/sift-bin/format.pl-149-
sift-4.0.3b/web/sift-bin/format.pl:150:system ("rm -f $tmp/$pid.comments*");
sift-4.0.3b/web/sift-bin/format.pl:151:system ("rm -f $tmp/$pid.tmp");
sift-4.0.3b/web/sift-bin/format.pl-152-
sift-4.0.3b/web/sift-bin/format.pl:153:#system ("rm -f $tmp/$pid*");
sift-4.0.3b/web/sift-bin/format.pl:154:#system ("rm -f $tmp/*$pid");
sift-4.0.3b/web/sift-bin/format.pl-155-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-92-print "<PRE>";
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl:93:system("$program_call $pid related_seqs $unalignedseq $out 27 $subst_file $gap_option $seq_identity_filter > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-94-
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl:95:@error_files = `ls $tmp/$$.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-96-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-104-
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl:105:# system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-106-# exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-125-
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl:126:$no_table_files = `ls $tmp/$$.aatable*|grep -v html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-127-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-153-
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl:154:system ("rm -f $tmp/$$.comments*");
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl:155:system ("rm -f $tmp/$$.tmp");
sift-4.0.3b/web/sift-bin/SIFT_related_seqs_submit.pl-156-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-88-if ($address ne "") {
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl:89: system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-90- print "Results will be mailed to $address.<BR>\n";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-92- # Put it in the SIFT2 (not SIFT) queue
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl:93: system("./add_queue_entry.pl SIFT2_queue $program_call $pid NCBI_blink $names{gi_number} $out 0 $subst_file 0 $seq_identity_filter $sequences_to_select $address > $comments 2> /dev/null");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-94- exit(0);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-106-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl:107: system("$program_call $pid NCBI_blink $names{gi_number} $out 0 $subst_file 0 $seq_identity_filter $sequences_to_select $address > $comments 2>&1");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-108-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-113-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl:114:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-115-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-133-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl:134:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-135-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-153-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl:154:system ("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-155-#errors or warnings that don't disrupt program
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-168-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl:169:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-170-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-175- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl:176: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_031508.pl-177- print "<A HREF=\"/pauline-bin/catfile.csh?btest-tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-39-#mkdir $tmp;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:40:#system("chmod 777 * -R $tmp");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-41-my $all_chr_file = @ARGV[2];
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-53-#Creat binned SNP files for SNP Classifier - the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:54:system("$bin/map_choords_to_chr_bin.pl $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-55-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-79- ### comment this block if using in operator see below.
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:80: #$sth_db_chr = $db_chr->prepare("select * from chr$chr where chr = \'chr$chr\' AND COORD2 = ?");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-81- #$sth_db_chr->execute("$coord2");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-85- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:86: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-87- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-92- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:93: $sth_db_chr = $db_chr->prepare("select * from chr$chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-94- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-98- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:99: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-100- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-124- push @ {$index_query_result{$key}}, $row;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:125: #system("echo $row >> $tmp/$pid.remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-126-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-212- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:213: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-214- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-364-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:365:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-366-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-368- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:369:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-370- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-495-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:496:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-497-if ($last_partition == 1){
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-498- for ($i = $master_pid + 1; $i <= $pid; $i ++){
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:499: system("cat $tmp/$i.combined_siftresults.predictions.table.html >> $tmp/$master_pid.combined_siftresults.predictions.table.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:500: system("cat $tmp/$i.combined_siftresults.predictions.tsv >> $tmp/$master_pid.combined_siftresults.predictions.tsv");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-501- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-568- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:569: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-570- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-765- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl:766: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_single_db_submit.pl-767-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-94-$program_call = $bin . "/SIFTING2.csh";
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl:95:system("$program_call $$ alignedseqs $alignedseq $out 27 $subst_file $gap_option $exp_option > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-96-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-116-#print "</PRE>";
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl:117:@error_files = `ls $tmp/$$.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-118-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-129- }
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl:130: system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-131- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-133-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl:134:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-135-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl:136:@table_files = `ls $tmp/$$.aatable*`;
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-137-$subject = "\"SIFT results\""; # literal double quotes for mailx
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-167-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl:168:system ("rm -f $tmp/$$.comments*");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl:169:system ("rm -f $tmp/$$.tmp");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit2.pl-170-
##############################################
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-101-select (STDOUT); $| = 1;
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl:102: system("$program_call $pid NCBI_blink $names{gi_number} $out 0 $subst_file 0 $seq_identity_filter $sequences_to_select $address > $comments 2>&1");
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl:103: system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-104-
##############################################
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-109-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl:110:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-111-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-129-
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl:130:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-131-
##############################################
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-149-
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl:150:system ("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-151-#errors or warnings that don't disrupt program
##############################################
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-164-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl:165:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-166-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-171- print "<BR>";
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl:172: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-173- print "<A HREF=\"/pauline-bin/catfile.csh?btest-tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-365- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl:366: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/an_example_of_IP.pl-367-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-81-select (STDOUT); $| = 1;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak:82: system("$program_call $pid NCBI_blink $names{gi_number} $out 0 $subst_file 0 $seq_identity_filter $sequences_to_select $address > $comments 2>&1");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak:83: system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-84-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-88-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak:89:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-90-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-108-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak:109:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-110-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-128-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak:129:system ("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-130-#errors or warnings that don't disrupt program
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-143-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak:144:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-145-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-150- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak:151: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bak-152- print "<A HREF=\"/pauline-bin/catfile.csh?btest-tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-18-#mkdir $tmp;
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl:19:#system("chmod 777 * -R $tmp");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-20-# output the beginning text to be used on all pages
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-155- close (CHR_FILE_NEW);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl:156: system("mv $all_chr_file.new $all_chr_file");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-157-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-197-if ($job_size == 0){
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl:198: system("rm -f $tmp/$new_pid.chrfile");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-199- print OUTPAGE "<tr BGCOLOR=\"\#DCDCDC\"><td>Complete set</td>";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-230-close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl:231:#system("cp $tmp/$pid.outpage.html $tmp/$pid.outpage.swap.html");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-232-#direct to the outpage url
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-246-}
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl:247:system("$bin/SIFT_feed_to_chr_coords_batch.pl $tmp/$pid.batchfile");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_prod.pl-248-close (BATCH_FILE);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi-82-print "Results will also be mailed to $address.<BR><BR>\n";
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi:83:#system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi-84-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi-369- my ($protein) = @_;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi:370: my $all_hits_alignment_file = `ls /home/sift/BLink_alignments/Predictions_ALL_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi-371-
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi:372: my $best_hits_alignment_file = `ls /home/sift/BLink_alignments/Predictions_BEST_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi-373- chomp ($all_hits_alignment_file);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi-377- my $newfile2 = "/home/sift/tmp/". $protein . ".besthits.msf";
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi:378: system ("cp $all_hits_alignment_file $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi:379: system ("cp $best_hits_alignment_file $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi:380: system ("chmod 660 $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi:381: system ("chmod 660 $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.cgi-382-#print HTML_OUT "newfile1 is $newfile1 newfile2 $newfile2<BR>\n";
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh-80-#option 1 for clumping to minimize work gibbs has to do
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh:81:@ clustered_seq = (`$srcdir/clump $query.globalX $tmpdir/$pid.clumped .9 1 | awk '{print $5}'`)
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh-82-echo "clumpint $clustered_seq"
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh-86- echo "Reclumping..."
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh:87: @ clustered_seq = (`$srcdir/clump $query.globalX $tmpdir/$pid.clumped .9 0 | awk '{print $5}'`)
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh-88- echo "GIBBS and motif on $clustered_seq sequences"
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh-95-cd $tmpdir
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh:96:set d = (`./protomat.csh $tmpdir/$pid.clumped`)
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block_backup.csh-97-echo $d
##############################################
sift-4.0.3b/web/sift-bin/contact.pl-121-close(BLK);
sift-4.0.3b/web/sift-bin/contact.pl:122:system("mutt -F /opt/www/sift/htdocs/.muttrc -s \"SIFT COMMENT for $$\" $siftmaster1 $siftmaster2 < $com");
sift-4.0.3b/web/sift-bin/contact.pl-123-print "<P>Thank you for your comment.<P>\n";
##############################################
sift-4.0.3b/web/sift-bin/start_queue.sh-29-for q in $qs; do
sift-4.0.3b/web/sift-bin/start_queue.sh:30:# nq="`ps -fu sift | grep -c ${q}_queue`"
sift-4.0.3b/web/sift-bin/start_queue.sh:31: nq="`ps fu | grep ${q}_queue | grep -v grep| grep quit|wc -l`"
sift-4.0.3b/web/sift-bin/start_queue.sh-32- #echo "ps fu | grep ${q}_queue | grep -v grep| wc -l"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-128-
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl:129: #system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-130-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-152- close (MESSAGE);
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl:153: system("mutt -F /opt/www/sift/htdocs/.muttrc -a $tmp/$pid.tsv -s \"SIFT Results for Job ID $pid\" $address <$tmp/$pid.email_message.txt");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-154-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-598- #my $all_hits_alignment_file =
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl:599:#`ls /home/sift/BLink_alignments/Predictions_ALL_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-600-
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-601- #my $best_hits_alignment_file =
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl:602:#`ls /home/sift/BLink_alignments/Predictions_BEST_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-603- chomp($all_hits_alignment_file);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-608- my $newfile2 = "$tmp/" . $protein . ".besthits.msf";
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl:609: system("cp $all_hits_alignment_file $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl:610: system("cp $best_hits_alignment_file $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl:611: system("chmod 660 $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl:612: system("chmod 660 $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit.pl-613-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-8- $file = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm:9: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-10-if ($status ==0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-19- $file = $tmp . "/$pid" . ".siftresults.matrix";
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm:20: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-21-
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-22-#send predictions
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm:23: @table_files = `ls $tmp/$pid.aatable*`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-24- $index = 0;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-34- $index++;
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm:35: system("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-36- }
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-37-# mail any errors
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm:38: @error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-39- for $file (@error_files) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-41- $tempstring = "\"$subject\""; $subject = $tempstring;
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm:42: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-43- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-114-# START
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm:115:#$no_pic_files = `ls $tmp/$$.*.ps | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines2.pm-116-#print_logos_desc($no_pic_files, $$);
##############################################
sift-4.0.3b/web/sift-bin/rm.csh-12-
sift-4.0.3b/web/sift-bin/rm.csh:13:set tot = `wc -l in | awk '{print $1}'`
sift-4.0.3b/web/sift-bin/rm.csh-14-if ($tot > 960) then
##############################################
sift-4.0.3b/web/sift-bin/rm.csh-29-foreach list ($lists)
sift-4.0.3b/web/sift-bin/rm.csh:30: set cgs = (`cut -f1 $list`)
sift-4.0.3b/web/sift-bin/rm.csh-31- foreach cg ($cgs)
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-106- $program_call = $bin . "/SIFT.start2.csh";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:107: exec("$program_call $pid query_seq $queryseqfile $out 27 $subst_file 0 $exp_option $names{database} $address > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-108- exit;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-112- $file = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:113: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-114- print "mail $subject $return_address $address $file ";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-122-$program_call = $bin . "/SIFTING2.csh";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:123:#system("$program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:124:system("$program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} > $comments 2>&1");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:125:@error_files = `ls $tmp/$$.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-126-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-137- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:138: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-139- print "<A HREF=\"/sift-bin/catfile.csh?$tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-141- }
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:142:# system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-143- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-150-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:151:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-152-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-165-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:166:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-167-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-230-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:231:system ("rm -f $tmp/$$.comments*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:232:system ("rm -f $tmp/$$.tmp");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-233-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:234:#system ("rm -f $tmp/$$*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig:235:#system ("rm -f $tmp/*$$");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.orig-236-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl-81-print "Results will also be mailed to $address.<BR><BR>\n";
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl:82:#system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl-83-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl-364- my ($protein) = @_;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl:365: my $all_hits_alignment_file = `ls /home/sift/BLink_alignments/Predictions_ALL_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl-366-
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl:367: my $best_hits_alignment_file = `ls /home/sift/BLink_alignments/Predictions_BEST_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl-368- chomp ($all_hits_alignment_file);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl-372- my $newfile2 = "/home/sift/tmp/". $protein . ".besthits.msf";
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl:373: system ("cp $all_hits_alignment_file $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl:374: system ("cp $best_hits_alignment_file $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl:375: system ("chmod 660 $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl:376: system ("chmod 660 $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_flatfile.pl-377-#print HTML_OUT "newfile1 is $newfile1 newfile2 $newfile2<BR>\n";
##############################################
sift-4.0.3b/web/sift-bin/protomat_motif.csh-67-
sift-4.0.3b/web/sift-bin/protomat_motif.csh:68:set minlen = (`grep " MINIMUM" $name.motifj.pros | awk '{print $2}'`)
sift-4.0.3b/web/sift-bin/protomat_motif.csh-69-if ($minlen < 8) then
##############################################
sift-4.0.3b/web/sift-bin/protomat_motif.csh-73- # Model heuristic; needs MINIMUM sequence length from $name.motifj.pros
sift-4.0.3b/web/sift-bin/protomat_motif.csh:74: set model = (`$protomat_bindir/model.run $name.motifj.pros`)
sift-4.0.3b/web/sift-bin/protomat_motif.csh-75- $protomat_bindir/gibbs $name.motifj.pros $model -f -s3 >& $name.gblks
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2March272004.pl-116- #NOTE: Results are actually mailed by $program_call
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2March272004.pl:117: system("./add_queue_entry.pl SIFT_queue $program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2March272004.pl-118-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2March272004.pl-120-{
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2March272004.pl:121: system("$program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2>&1 &");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2March272004.pl-122-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-51-#Creat binned SNP files for querying human chr database- the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:52:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-53-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-65- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:66: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-67- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-89- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:90: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-91- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-96- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:97: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:98: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-99- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-103- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:104: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-105- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-186- $row2 = "$row\t$ensg\t$gene_name\t$gene_desc\t$ensfm\t$fam_desc\t$gene_status\t$fam_size\t$kaks_mouse\t$kaks_macaque\t$mim_status\t$freq_av\t$freq_ceu";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:187: #system("echo $row2 >> $tmp/remove1");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-188- $key = "$chr\t$coord1\t$coord2\t$CDS\t$ensp_exists";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-294- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:295: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-296- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-506-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:507:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-508-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-510- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:511:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-512- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-601-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:602:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-603-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-764- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:765: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-766- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-808- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:809: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-810- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-1099- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl:1100: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_012510.pl-1101-
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.csh-108-#option 1 for clumping to minimize work gibbs has to do
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.csh:109:@ clustered_seq = (`$srcdir/clump $query.globalX $tmpdir/$pid.clumped .9 1 | awk '{print $5}'`)
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.csh-110-echo "clumpint $clustered_seq"
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.csh-114- echo "Reclumping..."
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.csh:115: @ clustered_seq = (`$srcdir/clump $query.globalX $tmpdir/$pid.clumped .9 0 | awk '{print $5}'`)
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.csh-116- echo "GIBBS and motif on $clustered_seq sequences"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-118- {
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:119:# system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-120- #NOTE: Results are actually mailed by $program_call
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-125- # Put it in the queue
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:126: system("./add_queue_entry.pl SIFT_queue $program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2> /dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-127-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-129-{
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:130: system("echo SIFT_queue $program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:131: system("$program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2>&1");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-132-# Pauline commented out background &");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-138-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:139:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-140-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-157-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:158:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-159-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-175-print "<BR>\n";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:176:system ("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-177-#errors or warnings that don't disrupt program
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-190-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:191:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-192-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-202- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl:203: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2_old.pl-204- print "<A HREF=\"/pauline-bin/catfile.csh?btest-tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-122-#check input validity and reformat chrfile
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl:123:system("$reformat_chrfile $all_chr_file");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-124-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-125-#Creat binned SNP files for SNP Classifier
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl:126:system("$bin/map_choords_to_bin_indels.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-127-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-233- if (-e $original_seq && -e $modified_seq){
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl:234: @indel_result = split /\t/, `$detect_indel $original_seq $modified_seq $outfile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-235- $aa_coords_original = $indel_result[0];
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-254-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl:255:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-256-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-258- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl:259:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-260- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-612- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl:613: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_indels_submit_bkp.pl-614-
##############################################
sift-4.0.3b/web/sift-bin/email_sift_aatable_results.pl-12-
sift-4.0.3b/web/sift-bin/email_sift_aatable_results.pl:13:$num_tables = `ls $tmp/$pid.aatable* | grep -v html | wc -l`;
sift-4.0.3b/web/sift-bin/email_sift_aatable_results.pl-14-
##############################################
sift-4.0.3b/web/sift-bin/email_sift_aatable_results.pl-27-" -a $tmp/$pid.aatable.html.zip -s \"SIFT Results for Job ID $pid\" $address <$tmp/$pid.email_message.txt";
sift-4.0.3b/web/sift-bin/email_sift_aatable_results.pl:28: system("$mutt_command");
sift-4.0.3b/web/sift-bin/email_sift_aatable_results.pl-29-
##############################################
sift-4.0.3b/web/sift-bin/contact_old.pl-126-{
sift-4.0.3b/web/sift-bin/contact_old.pl:127: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $siftmaster < $com");
sift-4.0.3b/web/sift-bin/contact_old.pl-128-}
##############################################
sift-4.0.3b/web/sift-bin/contact_old.pl-130-{
sift-4.0.3b/web/sift-bin/contact_old.pl:131: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $lamamaster < $com");
sift-4.0.3b/web/sift-bin/contact_old.pl-132-}
##############################################
sift-4.0.3b/web/sift-bin/contact_old.pl-134-{
sift-4.0.3b/web/sift-bin/contact_old.pl:135: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $webmaster < $com");
sift-4.0.3b/web/sift-bin/contact_old.pl-136-}
##############################################
sift-4.0.3b/web/sift-bin/clean_tmp.csh.bak-17-# Get tmp file dates - awk is $8 for howard, $9 for morgan
sift-4.0.3b/web/sift-bin/clean_tmp.csh.bak:18: set files = (`ls -ldt $tmpdir/$c* | tr -s ' ' ' ' | grep -v "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_tmp.csh.bak-19- foreach file ($files)
##############################################
sift-4.0.3b/web/sift-bin/clean_tmp.csh.bak-23-end
sift-4.0.3b/web/sift-bin/clean_tmp.csh.bak:24:set files = (`ls -ldt $tmpdir/[A-Z]* | tr -s ' ' ' ' | grep -v "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_tmp.csh.bak-25-foreach file ($files)
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-90-#Creat binned SNP files for SNP Classifier - the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:91:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-92-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-121- chop $coord2_str;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:122: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:123: #print "select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-124- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-129-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:130: system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-131-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-420-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:421:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-422-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-424- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:425:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-426- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-488- $address_aln_enst = "$datadir\/" . @rows_enst_address[0];
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:489: system("cp $address_aln_enst $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-490- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-509- print "</PRE>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:510: system("rm -f $tmp/$pid.$enst.substfile ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:511: system("rm -f $alignedfasta $alignedfasta.2 $alignedfasta.gapsremoved");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:512: system("rm -f $tmp/$pid.$enst.siftresults.matrix");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-513-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-518- #$psiblastout = $alignedfasta;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:519: #$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-520- #$seqno--; # subtract the QUERY sequence
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-521-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:522: #system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-523-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-952- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl:953: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bin_query.pl-954-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-94-#Creat binned SNP files for querying human chr database- the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:95:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-96-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-108- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:109: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-110- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-139- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:140: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-141- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-147- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:148: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:149: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-150- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-154- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:155: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-156- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-257- $row2 = "$row\t$ensg\t$gene_name\t$gene_desc\t$ensfm\t$fam_desc\t$gene_status\t$fam_size\t$kaks_mouse\t$kaks_macaque\t$mim_status\t$freq_av\t$freq_ceu";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:258: #system("echo $row2 >> $tmp/remove1");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-259- $key = "$chr\t$coord1\t$coord2\t$CDS\t$ensp_exists";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-340- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:341: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-342- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-616-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:617:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-618-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-801- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:802: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-803- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-846- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:847: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-848- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-1138- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:1139: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-1140-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-1272- my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:1273:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-1274-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-1276- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl:1277:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit.pl-1278- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl-139-
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl:140: system ("sort -k1,1 -k4,4n -k5,5n $new_chr_file > $all_chr_file.sorted");
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl:141:my @lines_to_get = `$bin/IntersectLocations.sh $all_chr_file.sorted gff $coding_file gff simple | grep -v Total | cut -f1 | uniq`;
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl-142-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl-461- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl:462: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl-463-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl-488- my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl:489: `cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl-490- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl-492- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl:493: `cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_intersect_cds_submit.pl-494- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/Classify_SNPs_Indels.pl-813- my $stmpfile = "tmp008";
sift-4.0.3b/web/sift-bin/Classify_SNPs_Indels.pl:814: system ("echo \">query\n$query_seq\n\" > $qtmpfile");
sift-4.0.3b/web/sift-bin/Classify_SNPs_Indels.pl:815: system ("echo \">subject\n$subject_seq\n\" > $stmpfile");
sift-4.0.3b/web/sift-bin/Classify_SNPs_Indels.pl:816: my $result = `blast -p blastp -i $qtmpfile -j $stmpfile`; # | grep Identities | head -n 1`;
sift-4.0.3b/web/sift-bin/Classify_SNPs_Indels.pl-817-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-18-#mkdir $tmp;
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl:19:#system("chmod 777 * -R $tmp");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-20-# output the beginning text to be used on all pages
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-168- close (CHR_FILE_NEW);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl:169: system("mv $all_chr_file.new $all_chr_file");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-170-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-210-if ($job_size == 0){
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl:211: system("rm -f $tmp/$new_pid.chrfile");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-212- print OUTPAGE "<tr BGCOLOR=\"\#DCDCDC\"><td>Complete set</td>";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-243-close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl:244:#system("cp $tmp/$pid.outpage.html $tmp/$pid.outpage.swap.html");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-245-#direct to the outpage url
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-259-}
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl:260:system("$bin/SIFT_feed_to_chr_coords_batch.pl $tmp/$pid.batchfile");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_bkp.pl-261-close (BATCH_FILE);
##############################################
sift-4.0.3b/web/sift-bin/test.pl-10- $pid = $$;
sift-4.0.3b/web/sift-bin/test.pl:11: system("./add_queue_entry.pl SIFT_queue $program_call $tmpdir/$pid.* > $tmpdir/$pid.test 2>/dev/null");
sift-4.0.3b/web/sift-bin/test.pl-12-
##############################################
sift-4.0.3b/web/sift-bin/snpfile_to_gff.pl-34-close (GFFFILE);
sift-4.0.3b/web/sift-bin/snpfile_to_gff.pl:35:system ("sort -k1,1 -k4,4n -k5,5n $snpfile.journal > $snpfile.gff");
sift-4.0.3b/web/sift-bin/snpfile_to_gff.pl-36-unlink("$snpfile.journal");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-72-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:73:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-74-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-76- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:77:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-78- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-129-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:130:#system("echo $bin/add_queue_entry.pl $queuedir/$queue $program_call $pid NCBI_blink $names{gi_number} $out 0 $subst_file 0 $seq_identity_filter $sequences_to_select $address > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-131-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-132-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:133:system("$bin/add_queue_entry.pl $queuedir/$queue $program_call $pid NCBI_blink $names{gi_number} $out 0 $subst_file 0 $seq_identity_filter $sequences_to_select $address > $comments 2>&1");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-134-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-138-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:139:# system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-140-print "</PRE>";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-154-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:155:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-156-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-176-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:177: $no_table_files = `ls $tmp/$$.aatable* | grep -v html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-178-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-196-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:197:system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-198-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-214-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:215:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-216-if ( @error_files > 0 ) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-222- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:223: system("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-224- print
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-237-#email the results
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:238:$num_tables = `ls $tmp/$$.aatable*.html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-239-if ($address ne ""){
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-249- $mutt_command.=" -s \"SIFT Results for Job ID $pid\" $address <$tmp/$pid.email_message.txt";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:250: system("$mutt_command");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-251-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-445- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl:446: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl-447-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-94-$program_call = $bin . "/SIFTING.csh";
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl:95:system("$program_call $$ alignedseqs $alignedseq $out 27 $subst_file $gap_option $exp_option > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-96-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl:97:@error_files = `ls $tmp/$$.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-98-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-105- }
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl:106: system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-107- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-109-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl:110:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-111-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-142-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl:143:system ("rm -f $tmp/$$.comments*");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl:144:system ("rm -f $tmp/$$.tmp");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submitbackup.pl-145-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-122-#Creat binned SNP files for SNP Classifier
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl:123:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-124-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-310-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl:311:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-312-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-314- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl:315:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-316- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-391- $alignedfasta = "$tmp\/$pid\.$gi.alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl:392: system("cp $address_aln_best $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-393- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-416- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl:417: system("cp $address_aln_all $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-418- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-436- $psiblastout = $alignedfasta;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl:437: $seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-438- $seqno--; # subtract the QUERY sequence
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-439-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl:440: system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-441-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-886- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl:887: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_no_binning.pl-888-
##############################################
sift-4.0.3b/web/sift-bin/write_IP_logfile.pl-23-# lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/write_IP_logfile.pl:24:`./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/write_IP_logfile.pl-25-
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl-55-
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl:56:system("$bin/seq_to_subfamily_block.csh $query $names{database} > $out 2>/dev/null");
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl-57-
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl-64-#print "check out $$<BR>";
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl:65:@error_files = `ls $tmp/$$.*.error`;
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl-66-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl-73- }
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl:74: system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl-75- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl-86-
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl:87:#system ("rm -f $tmp/$$*");
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl:88:#system ("rm -f $tmp/*$$");
sift-4.0.3b/web/sift-bin/seq_to_subfamily_block.pl-89-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-51-#Creat binned SNP files for SNP Classifier - the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:52:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-53-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-65- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:66: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-67- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-89- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:90: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-91- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-96- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:97: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:98: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-99- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-103- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:104: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-105- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-129- push @ {$index_query_result{$key}}, $row;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:130: #system("echo $row >> $tmp/$pid.remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-131-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-221- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:222: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-223- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-373-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:374:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-375-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-377- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:378:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-379- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-516-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:517:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-518-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-667- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:668: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-669- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-711- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:712: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-713- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-908- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl:909: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_prod.pl-910-
##############################################
sift-4.0.3b/web/sift-bin/PHAT_submission.pl-110-
sift-4.0.3b/web/sift-bin/PHAT_submission.pl:111:system("$bin/fastaseqs $query $queryclean > /dev/null");
sift-4.0.3b/web/sift-bin/PHAT_submission.pl:112:system ("$bin/fastaseqs $dbase $dbaseclean > /dev/null");
sift-4.0.3b/web/sift-bin/PHAT_submission.pl-113-
sift-4.0.3b/web/sift-bin/PHAT_submission.pl-114-
sift-4.0.3b/web/sift-bin/PHAT_submission.pl:115:#system("$bin/PHAT_submission.csh $queryclean $txmem $dbaseclean $nontxmem_matrix $txmem_matrix > $out 2>&1");
sift-4.0.3b/web/sift-bin/PHAT_submission.pl-116-
sift-4.0.3b/web/sift-bin/PHAT_submission.pl:117:system("$bin/PHAT_submission.csh $queryclean $txmem $dbaseclean $nontxmem_matrix $txmem_matrix > $out 2>/dev/null");
sift-4.0.3b/web/sift-bin/PHAT_submission.pl-118-
##############################################
sift-4.0.3b/web/sift-bin/PHAT_submission.pl-156-
sift-4.0.3b/web/sift-bin/PHAT_submission.pl:157:system ("rm $out");
sift-4.0.3b/web/sift-bin/PHAT_submission.pl-158-
##############################################
sift-4.0.3b/web/sift-bin/clean.pl-18-
sift-4.0.3b/web/sift-bin/clean.pl:19:system("ls -t ../tmp > $tmp");
sift-4.0.3b/web/sift-bin/clean.pl-20-
##############################################
sift-4.0.3b/web/sift-bin/clean.pl-28- if ((-T $file) && ((-M $file) > $days))
sift-4.0.3b/web/sift-bin/clean.pl:29: { system("rm -f $file"); }
sift-4.0.3b/web/sift-bin/clean.pl-30-# { print "$file\n"; }
##############################################
sift-4.0.3b/web/sift-bin/clean.pl-32-close(IN);
sift-4.0.3b/web/sift-bin/clean.pl:33:system("rm -f $tmp");
sift-4.0.3b/web/sift-bin/clean.pl-34-exit(0);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-8- $file = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak:9: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-10-if ($status ==0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-19- $file = $tmp . "/$pid" . ".siftresults.matrix";
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak:20: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-21-
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-22-#send predictions
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak:23: @table_files = `ls $tmp/$pid.aatable*`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-24- $index = 0;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-34- $index++;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak:35: system("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-36- }
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-37-# mail any errors
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak:38: @error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-39- for $file (@error_files) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-41- $tempstring = "\"$subject\""; $subject = $tempstring;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak:42: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-43- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-114-# START
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak:115:#$no_pic_files = `ls $tmp/$$.*.ps | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm.bak-116-#print_logos_desc($no_pic_files, $$);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-72-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:73:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-74-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-76- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:77:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-78- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-137-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:138:# system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-139-print "</PRE>";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-153-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:154:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-155-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-175-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:176: $no_table_files = `ls $tmp/$$.aatable* | grep -v html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-177-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-195-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:196:system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-197-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-213-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:214:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-215-if ( @error_files > 0 ) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-221- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:222: system("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-223- print
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-236-#email the results
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:237:$num_tables = `ls $tmp/$$.aatable*.html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-238-if ($address ne ""){
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-248- $mutt_command.=" -s \"SIFT Results for Job ID $pid\" $address <$tmp/$pid.email_message.txt";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:249: system("$mutt_command");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-250-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-444- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl:445: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit_old.pl-446-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-99-$program_call = $bin . "/SIFTING2.csh";
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl:100:system("$program_call $pid alignedseqs $alignedseq $out 27 $subst_file $gap_option $seq_identity_filter > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-101-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-114-#print "</PRE>";
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl:115:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-116-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-127- }
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl:128:# system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-129- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-131-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl:132:$no_table_files = `ls $tmp/$pid.aatable* |grep -v html| wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-133-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-135-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl:136:@table_files = `ls $tmp/$pid.aatable*`;
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-137-$subject = "\"SIFT results\""; # literal double quotes for mailx
##############################################
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-167-
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl:168:#system ("rm -f $tmp/$$.comments*");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl:169:#system ("rm -f $tmp/$$.tmp");
sift-4.0.3b/web/sift-bin/SIFT_aligned_seqs_submit.pl-170-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-52-#Creat binned SNP files for querying human chr database- the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:53:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-54-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-66- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:67: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-68- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-90- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:91: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-92- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-97- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:98: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:99: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-100- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-104- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:105: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-106- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-187- $row2 = "$row\t$ensg\t$gene_name\t$gene_desc\t$ensfm\t$fam_desc\t$gene_status\t$fam_size\t$kaks_mouse\t$kaks_macaque\t$mim_status\t$freq_av\t$freq_ceu";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:188: #system("echo $row2 >> $tmp/remove1");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-189- $key = "$chr\t$coord1\t$coord2\t$CDS\t$ensp_exists";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-295- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:296: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-297- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-499-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:500:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-501-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-503- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:504:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-505- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-581-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:582:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-583-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-740- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:741: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-742- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-784- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:785: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-786- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-1081- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl:1082: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_bkp.pl-1083-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-114-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:115:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-116-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-120- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:121:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-122- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-153-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:154: # system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-155- #NOTE: Results are actually mailed by $program_call
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-161-# Put it in the queue
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:162:#system("./add_queue_entry.pl SIFT_queue $program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2> /dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-163- system(
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-168-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:169:#system("echo $program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-170- system(
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-183-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:184:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-185-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-202-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:203:$no_table_files = `ls $tmp/$$.aatable* |grep -v html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-204-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-219-print "<BR>\n";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:220:system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-221-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-237-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:238:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-239-if ( @error_files > 0 ) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-250- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:251: system("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-252- print
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-262-#email the results
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:263:$num_tables = `ls $tmp/$$.aatable*.html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-264-if ( $address ne "" ) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-277-" -s \"SIFT Results for Job ID $pid\" $address <$tmp/$pid.email_message.txt";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl:278: #system("$mutt_command");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl-279-}
##############################################
sift-4.0.3b/web/sift-bin/add_queue_entry.pl-25-# lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/add_queue_entry.pl:26:`$lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/add_queue_entry.pl-27-# append the address and command to the queue file
##############################################
sift-4.0.3b/web/sift-bin/add_queue_entry.pl-29-print FILE "@ARGV\n";
sift-4.0.3b/web/sift-bin/add_queue_entry.pl:30:#system("more $queuefile > $tmp/remove");
sift-4.0.3b/web/sift-bin/add_queue_entry.pl:31:#system ("echo @ARGV > $tmp/remove");
sift-4.0.3b/web/sift-bin/add_queue_entry.pl:32:#system ("more $queuefile > $tmp/remove1");
sift-4.0.3b/web/sift-bin/add_queue_entry.pl-33-close(FILE);
##############################################
sift-4.0.3b/web/sift-bin/add_queue_entry.pl-44- if ($num_queues != 2){
sift-4.0.3b/web/sift-bin/add_queue_entry.pl:45: system ("$bin/start_queue.sh");
sift-4.0.3b/web/sift-bin/add_queue_entry.pl-46- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-121-#Creat binned SNP files for SNP Classifier - the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:122:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-123-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-145- $nt2b = $2;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:146: print "select * from $table_chr where chr = \'chr$chr\' AND COORD1 = $coord1 and COORD2 = $coord2 AND nt2 = \'$nt2b\' AND CDS = 1 AND ENSP <> \'\'";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:147: $sth_db_chr_CDS = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = $coord1 and COORD2 = $coord2 AND nt2 = \'$nt2b\' AND CDS = 1 AND ENSP <> \'\'");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:148: $sth_db_chr_no_CDS = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = $coord1 and COORD2 = $coord2 and (nt1 = \'$nt2a\' or nt1 = \'$nt2b\') AND CDS = 0 ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-149- $sth_db_chr_CDS->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-171- $coord_result_no_CDS_hash{"$chr\t$coord1\t$coord2\t$orn_usr\t$alleles"} = $result;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:172: system("echo $chr\t$coord1\t$coord2\t$orn_usr\t$alleles >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-173-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-190- $coord_result_no_CDS_hash{"$chr\t$coord1\t$coord2\t$orn_db\t$alleles"} = $result;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:191: system("echo $chr\t$coord1\t$coord2\t$orn_db\t$alleles >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-192- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-211- $coord_result_CDS_hash{"$chr\t$coord1\t$coord2\t$orn_db\t$alleles_db"} = $result;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:212: system("echo $chr\t$coord1\t$coord2\t$orn_db\t$alleles_db >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-213- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-294-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:295:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-296-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-298- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:299:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-300- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-362- $address_aln_enst = "$datadir\/" . @rows_enst_address[0];
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:363: system("cp $address_aln_enst $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-364- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-388- $psiblastout = $alignedfasta;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:389: $seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-390- $seqno--; # subtract the QUERY sequence
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-391-
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:392: system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-393-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-822- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl:823: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_1_by_1_db_query.pl-824-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl-164- close (CHR_FILE_NEW);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl:165: system("mv $all_chr_file.new $all_chr_file");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl-166-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl-206-if ($job_size == 0){
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl:207: system("rm -f $tmp/$new_pid.chrfile");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl-208- print OUTPAGE "<tr BGCOLOR=\"\#DCDCDC\"><td>Complete set</td>";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl-239-close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl:240:#system("cp $tmp/$pid.outpage.html $tmp/$pid.outpage.swap.html");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl-241-#direct to the outpage url
##############################################
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl-255-}
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl:256:system("$bin/SIFT_feed_to_chr_coords_batch.pl $tmp/$pid.batchfile");
sift-4.0.3b/web/sift-bin/SIFT_feed_to_chr_coords_check.pl-257-close (BATCH_FILE);
##############################################
sift-4.0.3b/web/sift-bin/clean_hour.csh-19-echo $hdate
sift-4.0.3b/web/sift-bin/clean_hour.csh:20:set hour = `echo $hdate | awk '{print $3}'`
sift-4.0.3b/web/sift-bin/clean_hour.csh-21-#echo $hour
##############################################
sift-4.0.3b/web/sift-bin/clean_hour.csh-25-while ($c >= 100)
sift-4.0.3b/web/sift-bin/clean_hour.csh:26:# set files = (`ls -ldt ~/tmp/$c* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $8}'`)
sift-4.0.3b/web/sift-bin/clean_hour.csh:27:# set times = (`ls -ldt ~/tmp/$c* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $7}'`)
sift-4.0.3b/web/sift-bin/clean_hour.csh:28: set files = (`ls -ldt ~/tmp/$c*.err ~/tmp/$c*.seq* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $8}'`)
sift-4.0.3b/web/sift-bin/clean_hour.csh:29: set times = (`ls -ldt ~/tmp/$c*.err ~/tmp/$c*.seq* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $7}'`)
sift-4.0.3b/web/sift-bin/clean_hour.csh-30- @ i = 0
##############################################
sift-4.0.3b/web/sift-bin/clean_hour.csh-32-# echo "$i $files[$i] $times[$i]"
sift-4.0.3b/web/sift-bin/clean_hour.csh:33: set h = `echo $times[$i] | awk -F: '{print $1}'`
sift-4.0.3b/web/sift-bin/clean_hour.csh-34- if ($h < $hour) then
##############################################
sift-4.0.3b/web/sift-bin/clean_hour.csh-43-while ($c >= 1)
sift-4.0.3b/web/sift-bin/clean_hour.csh:44: set files = (`ls -ldt ~/tmp/$c*.err ~/tmp/$c*.seq* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $8}'`)
sift-4.0.3b/web/sift-bin/clean_hour.csh:45: set times = (`ls -ldt ~/tmp/$c*.err ~/tmp/$c*.seq* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $7}'`)
sift-4.0.3b/web/sift-bin/clean_hour.csh-46- @ i = 0
##############################################
sift-4.0.3b/web/sift-bin/clean_hour.csh-48-# echo "$i $files[$i] $times[$i]"
sift-4.0.3b/web/sift-bin/clean_hour.csh:49: set h = `echo $times[$i] | awk -F: '{print $1}'`
sift-4.0.3b/web/sift-bin/clean_hour.csh-50- if ($h < $hour) then
##############################################
sift-4.0.3b/web/sift-bin/clean_am.csh-30-# Get today's tmp file dates - awk is $8 for howard, $9 for morgan
sift-4.0.3b/web/sift-bin/clean_am.csh:31: set files = (`ls -ldt $tmpdir/$c* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_am.csh-32- foreach file ($files)
sift-4.0.3b/web/sift-bin/clean_am.csh:33: set four = `ls -lgt $file | awk '{print $7}' | cut -d":" -f1`
sift-4.0.3b/web/sift-bin/clean_am.csh-34-#echo "four=$four"
##############################################
sift-4.0.3b/web/sift-bin/clean_am.csh-42-
sift-4.0.3b/web/sift-bin/clean_am.csh:43:set files = (`ls -ldt $tmpdir/[A-Z]* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_am.csh-44-foreach file ($files)
sift-4.0.3b/web/sift-bin/clean_am.csh:45: set four = `ls -lgt $file | awk '{print $7}' | cut -d":" -f1`
sift-4.0.3b/web/sift-bin/clean_am.csh-46- if ($four < $cut) then
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-66-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:67:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-68-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-70- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:71:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-72- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-116-);
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:117:# system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-118-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-123-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:124:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-125-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-144-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:145: $no_table_files = `ls $tmp/$$.aatable* | grep -v html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-146-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-164-
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:165:system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-166-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-182-# Pauline added printint error files
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:183:@error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-184-if ( @error_files > 0 ) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-190- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:191: system("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-192- print
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-205-#email the results
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:206:$num_tables = `ls $tmp/$$.aatable*.html | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-207-if ($address ne ""){
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-217- $mutt_command.=" -s \"SIFT Results for Job ID $pid\" $address <$tmp/$pid.email_message.txt";
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:218: system("$mutt_command");
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-219-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-413- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp:414: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_BLink_submit.pl.bkp-415-
##############################################
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl-27-
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl:28:my @predictions_files = `ls $tmp/$pid\.*.siftresults.predictions`;
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl-29-
##############################################
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl-107-
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl:108: system("\/usr\/bin\/mutt -F \/opt\/www\/sift\/htdocs\/.muttrc -a $tmp\/$pid\_predictions.tsv -s \"SIFT Results for Job ID $pid\" $address \< $tmp\/$pid.email_message.txt");
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl-109-}
##############################################
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl-301- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl:302: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/collate_SIFT_pid_subst.pl-303-
##############################################
sift-4.0.3b/web/sift-bin/indelfile_to_gff.pl-34-close (GFFFILE);
sift-4.0.3b/web/sift-bin/indelfile_to_gff.pl:35:system ("sort -k1,1 -k4,4n -k5,5n $snpfile.journal > $snpfile.gff");
sift-4.0.3b/web/sift-bin/indelfile_to_gff.pl-36-unlink("$snpfile.journal");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl-81-print "Results will also be mailed to $address.<BR><BR>\n";
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl:82:#system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl-83-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl-364- my ($protein) = @_;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl:365: my $all_hits_alignment_file = `ls /home/sift/BLink_alignments/Predictions_ALL_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl-366-
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl:367: my $best_hits_alignment_file = `ls /home/sift/BLink_alignments/Predictions_BEST_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl-368- chomp ($all_hits_alignment_file);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl-372- my $newfile2 = "/home/sift/tmp/". $protein . ".besthits.msf";
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl:373: system ("cp $all_hits_alignment_file $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl:374: system ("cp $best_hits_alignment_file $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl:375: system ("chmod 660 $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl:376: system ("chmod 660 $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_backup.pl-377-#print HTML_OUT "newfile1 is $newfile1 newfile2 $newfile2<BR>\n";
##############################################
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl-93-
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl:94:system("$bin/fastaseqs $query $queryclean > /dev/null");
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl-95-
##############################################
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl-97-
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl:98:#system("$bin/PHAT_submission.csh $queryclean $txmem $dbaseclean $nontxmem_matrix $txmem_matrix > $out 2>&1");
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl-99-
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl:100:system("$bin/PHAT_submission_profile.csh $queryclean $txmem $nontxmem_matrix $txmem_matrix > $out 2>/dev/null");
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl-101-
##############################################
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl-113-
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl:114:system ("rm $out");
sift-4.0.3b/web/sift-bin/PHAT_submission_profile.pl-115-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-14- $file = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm:15: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-16-if ($status ==0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-25- $file = $tmp . "/$pid" . ".siftresults.matrix";
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm:26: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-27-
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-28-#send predictions
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm:29: @table_files = `ls $tmp/$pid.aatable*`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-30- $index = 0;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-40- $index++;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm:41: system("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-42- }
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-43-# mail any errors
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm:44: @error_files = `ls $tmp/$pid.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-45- for $file (@error_files) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-47- $tempstring = "\"$subject\""; $subject = $tempstring;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm:48: system ("mailx -s $subject -r $return_address $address < $file");
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-49- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-120-# START
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm:121:#$no_pic_files = `ls $tmp/$$.*.ps | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_subroutines.pm-122-#print_logos_desc($no_pic_files, $$);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl-105-
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl:106: #system ("echo $address >> /home/sift/email_log");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl-107-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl-520- my $all_hits_alignment_file =
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl:521:`ls /home/sift/BLink_alignments/Predictions_ALL_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl-522-
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl-523- my $best_hits_alignment_file =
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl:524:`ls /home/sift/BLink_alignments/Predictions_BEST_HIT_Proteins/*/$protein*.msf`;
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl-525- chomp($all_hits_alignment_file);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl-530- my $newfile2 = "/home/sift/tmp/" . $protein . ".besthits.msf";
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl:531: system("cp $all_hits_alignment_file $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl:532: system("cp $best_hits_alignment_file $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl:533: system("chmod 660 $newfile2");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl:534: system("chmod 660 $newfile1");
sift-4.0.3b/web/sift-bin/SIFT_dbSNP_submit_db.pl-535-
##############################################
sift-4.0.3b/web/sift-bin/clean_tmp.csh-23-# Get tmp file dates - awk is $8 for howard, $9 for morgan
sift-4.0.3b/web/sift-bin/clean_tmp.csh:24: set files = (`ls -ldt $tmpdir/$c* | tr -s ' ' ' ' | grep -v "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_tmp.csh-25- foreach file ($files)
##############################################
sift-4.0.3b/web/sift-bin/clean_tmp.csh-28-
sift-4.0.3b/web/sift-bin/clean_tmp.csh:29: set files = (`ls -ldt $tmpdir/NP_${c}* | tr -s ' ' ' ' | grep -v "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_tmp.csh-30- foreach file ($files)
##############################################
sift-4.0.3b/web/sift-bin/clean_tmp.csh-36-
sift-4.0.3b/web/sift-bin/clean_tmp.csh:37:set files = (`ls -ldt $tmpdir/[A-Z]* | tr -s ' ' ' ' | grep -v "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_tmp.csh-38-foreach file ($files)
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-92-#Creat binned SNP files for querying human chr database- the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:93:system("$bin/map_choords_to_bin.pl $bin_file $all_chr_file $pid");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-94-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-106- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:107: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-108- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-137- #}
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:138: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-139- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-145- ### uncomment following block if using in operator - see above
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:146: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:147: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-148- $sth_db_chr->execute();
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-152- }
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:153: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-154- ###
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-255- $row2 = "$row\t$ensg\t$gene_name\t$gene_desc\t$ensfm\t$fam_desc\t$gene_status\t$fam_size\t$kaks_mouse\t$kaks_macaque\t$mim_status\t$freq_av\t$freq_ceu";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:256: #system("echo $row2 >> $tmp/remove1");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-257- $key = "$chr\t$coord1\t$coord2\t$CDS\t$ensp_exists";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-338- #print "$row<BR>";
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:339: #system("echo $row >> $tmp/remove");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-340- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-593-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:594:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-595-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-758- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:759: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-760- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-802- close (OUTPAGE);
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:803: system ("chmod 755 $tmp/$master_pid.outpage.modified.html");
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-804- rename "$tmp/$master_pid.outpage.modified.html", "$tmp/$master_pid.outpage.html"
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-1093- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:1094: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-1095-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-1227- my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:1228:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-1229-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-1231- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl:1232:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_chr_coords_submit_030110.pl-1233- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-112- # Put it in the queue
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:113: system("./add_queue_entry.pl SIFT_queue $program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-114- #NOTE: Results are actually mailed by $program_call
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-121-$program_call = $bin . "/SIFTING2.csh";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:122:#system("$program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:123:system("$program_call $pid query_seq $queryseqfile $out $info $subst_file 0 $seq_identity_filter $names{database} $address > $comments 2>&1");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:124:@error_files = `ls $tmp/$$.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-125-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-136- print "<BR>";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:137: system ("sed s/X/-/g $tmp/$pid.seq.query.globalX > $tmp/$pid.aln");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-138- print "<A HREF=\"/sift-bin/catfile.csh?$tmp/$pid.aln+Alignment+PRE\">";
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-140- }
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:141:# system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-142- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-150-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:151:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-152-$seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-165-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:166:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-167-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-230-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:231:system ("rm -f $tmp/$$.comments*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:232:system ("rm -f $tmp/$$.tmp");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-233-
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:234:#system ("rm -f $tmp/$$*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak:235:#system ("rm -f $tmp/*$$");
sift-4.0.3b/web/sift-bin/SIFT_seq_submit2.pl.bak-236-
##############################################
sift-4.0.3b/web/sift-bin/run_queue.pl-40-if (!(-e $queuefile)) {
sift-4.0.3b/web/sift-bin/run_queue.pl:41: `touch $queuefile`;
sift-4.0.3b/web/sift-bin/run_queue.pl-42-}
##############################################
sift-4.0.3b/web/sift-bin/run_queue.pl-54- $command = &readlineorsleep();
sift-4.0.3b/web/sift-bin/run_queue.pl:55: system($command);
sift-4.0.3b/web/sift-bin/run_queue.pl-56-}
##############################################
sift-4.0.3b/web/sift-bin/run_queue.pl-86- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/run_queue.pl:87: `$lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/run_queue.pl-88- open(TMPFILE, ">$tmpqueuefile");
##############################################
sift-4.0.3b/web/sift-bin/DNA_PROT_SUBROUTINES.pl-337-
sift-4.0.3b/web/sift-bin/DNA_PROT_SUBROUTINES.pl:338: my $seqtmp = `zcat $gz_chr_file | head -2 | tail -1`;
sift-4.0.3b/web/sift-bin/DNA_PROT_SUBROUTINES.pl-339- $_ = $seqtmp;
##############################################
sift-4.0.3b/web/sift-bin/DNA_PROT_SUBROUTINES.pl-352-
sift-4.0.3b/web/sift-bin/DNA_PROT_SUBROUTINES.pl:353: my @seq = `zcat $gz_chr_file | head -$linestart | tail -$numlines`;
sift-4.0.3b/web/sift-bin/DNA_PROT_SUBROUTINES.pl-354- my $basestart = $start_pos % $linewidth;
##############################################
sift-4.0.3b/web/sift-bin/clean_pm.csh-29-# Get today's tmp file dates - awk is $8 for howard, $9 for morgan
sift-4.0.3b/web/sift-bin/clean_pm.csh:30: set files = (`ls -ldt $tmpdir/$c* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_pm.csh-31- foreach file ($files)
sift-4.0.3b/web/sift-bin/clean_pm.csh:32: set four = `ls -lgt $file | awk '{print $7}' | cut -d":" -f1`
sift-4.0.3b/web/sift-bin/clean_pm.csh-33-#echo "four=$four"
##############################################
sift-4.0.3b/web/sift-bin/clean_pm.csh-41-
sift-4.0.3b/web/sift-bin/clean_pm.csh:42:set files = (`ls -ldt $tmpdir/[A-Z]* | tr -s ' ' ' ' | grep "$zdate" | awk '{print $9}'`)
sift-4.0.3b/web/sift-bin/clean_pm.csh-43-foreach file ($files)
sift-4.0.3b/web/sift-bin/clean_pm.csh:44: set four = `ls -lgt $file | awk '{print $7}' | cut -d":" -f1`
sift-4.0.3b/web/sift-bin/clean_pm.csh-45- if ($four < $cut) then
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-224-my $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:225:`cat /home/blocks/apache/logs/access_log | grep POST | grep $IP_address | wc -l `;
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-226-chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-228- $ip_counts =
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:229:`cat /home/blocks/apache/logs/access_log | grep POST | grep $remote_host | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-230- chomp($ip_counts);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-292- $alignedfasta = "$tmp\/$pid\.$gi.alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:293: system("cp $address_aln_best $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-294- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-313- }
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:314: system("cp $address_aln_all $alignedfasta");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-315- }
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-329- $psiblastout = $alignedfasta;
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:330: $seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-331- $seqno--; # subtract the QUERY sequence
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-333-
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:334: system("cat $tmp/$pid.*.error >> $tmp/$pid.err");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-335- #errors or warnings that don't disrupt program
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-366-foreach $gi (@gi_list){
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:367: system ("echo 'Protein Identifier: <b><u>$gi</u></b>' >> $tmp/$combined_siftresults_file.predictions");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:368: system ("cat $tmp/$pid.$gi.siftresults.predictions >> $tmp/$combined_siftresults_file.predictions");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-369-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-462-
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:463: system("\/usr\/bin\/mutt -F \/opt\/www\/sift\/htdocs\/.muttrc -a $tmp\/$pid\_predictions.tsv -s \"SIFT Results for Job ID $pid\" $address \< $tmp\/$pid.email_message.txt");
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-464-}
##############################################
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-656- # lockfile will wait until it can lock the file
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl:657: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/sift-bin/SIFT_pid_subst_all_submit.pl-658-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-89-print "<PRE>";
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:90:system("$program_call $pid query_seq $queryseqfile $out 27 $subst_file $gap_option $exp_option $names{database} > $comments 2>/dev/null");
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:91:@error_files = `ls $tmp/$$.*.error`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-92-if (@error_files > 0) {
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-99- }
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:100: system ("rm -f $tmp/$$.*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-101- exit (-1);
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-107-$psiblastout = $tmp . "/$pid" . ".alignedfasta";
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:108:$seqno = `grep ">" $psiblastout | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-109-$seqno--;
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-117-
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:118:$no_table_files = `ls $tmp/$$.aatable* | wc -l`;
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-119-
##############################################
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-153-
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:154:system ("rm -f $tmp/$$.comments*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:155:system ("rm -f $tmp/$$.tmp");
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-156-
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:157:#system ("rm -f $tmp/$$*");
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl:158:#system ("rm -f $tmp/*$$");
sift-4.0.3b/web/sift-bin/SIFT_seq_submitcopy.pl-159-
##############################################
sift-4.0.3b/web/blocks-bin/htmlize-getblock.pl-111-open(FPDB, ">../tmp/$$.pdbfile");
sift-4.0.3b/web/blocks-bin/htmlize-getblock.pl:112:system("chmod -f 660 ../tmp/$$.*");
sift-4.0.3b/web/blocks-bin/htmlize-getblock.pl-113-#
##############################################
sift-4.0.3b/web/blocks-bin/htmlize-getblock.pl-387-#$pdbtemp = "../tmp/$$.pdbmast";
sift-4.0.3b/web/blocks-bin/htmlize-getblock.pl:388:#system("grep \"^$group\" $pdbfile > $pdbtemp");
sift-4.0.3b/web/blocks-bin/htmlize-getblock.pl-389-if ($prints_flag > 0) { $pdbtemp = "../data-prints/pdbs/$group.pdb"; }
##############################################
sift-4.0.3b/web/blocks-bin/blalign.pl-48-
sift-4.0.3b/web/blocks-bin/blalign.pl:49:system("$bin/blalign $blk $names{style} > $tmp/$$.out");
sift-4.0.3b/web/blocks-bin/blalign.pl-50-
##############################################
sift-4.0.3b/web/blocks-bin/htmlize-getchrom.pl-125-open(FCYR, ">../tmp/$$.cyrca");
sift-4.0.3b/web/blocks-bin/htmlize-getchrom.pl:126:system("chmod -f 660 ../tmp/$$.*");
sift-4.0.3b/web/blocks-bin/htmlize-getchrom.pl-127-#
##############################################
sift-4.0.3b/web/blocks-bin/treeviewer.pl-144- open(BLK, ">$blkfile");
sift-4.0.3b/web/blocks-bin/treeviewer.pl:145: { print BLK param('blocks'); }
sift-4.0.3b/web/blocks-bin/treeviewer.pl-146- close(BLK);
##############################################
sift-4.0.3b/web/blocks-bin/treeviewer.pl-152- open(SEQ, ">$seqfile");
sift-4.0.3b/web/blocks-bin/treeviewer.pl:153: { print SEQ param('seqs'); }
sift-4.0.3b/web/blocks-bin/treeviewer.pl-154- close(SEQ);
##############################################
sift-4.0.3b/web/blocks-bin/treeviewer.pl-165- $blkflag = 1;
sift-4.0.3b/web/blocks-bin/treeviewer.pl:166: system("cp $blocksdir/blks/$family.blks $blkfile");
sift-4.0.3b/web/blocks-bin/treeviewer.pl-167- }
##############################################
sift-4.0.3b/web/blocks-bin/treeviewer.pl-170- $blkflag = 1;
sift-4.0.3b/web/blocks-bin/treeviewer.pl:171: system("cp $printsdir/blks/$family.blks $blkfile");
sift-4.0.3b/web/blocks-bin/treeviewer.pl-172- }
##############################################
sift-4.0.3b/web/blocks-bin/treeviewer.pl-178- $seqflag = 1;
sift-4.0.3b/web/blocks-bin/treeviewer.pl:179: system("cp $blocksdir/pros/$family.pros $seqfile");
sift-4.0.3b/web/blocks-bin/treeviewer.pl-180- }
##############################################
sift-4.0.3b/web/blocks-bin/treeviewer.pl-183- $seqflag = 1;
sift-4.0.3b/web/blocks-bin/treeviewer.pl:184: system("cp $printsdir/pros/$family.pros $seqfile");
sift-4.0.3b/web/blocks-bin/treeviewer.pl-185- }
##############################################
sift-4.0.3b/web/blocks-bin/treeviewer.pl-342- if (-s "$errfile") {
sift-4.0.3b/web/blocks-bin/treeviewer.pl:343: system("cat $errfile");
sift-4.0.3b/web/blocks-bin/treeviewer.pl-344- fatal("tree rendering failed.");
##############################################
sift-4.0.3b/web/blocks-bin/contact.pl-134-{
sift-4.0.3b/web/blocks-bin/contact.pl:135: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $siftmaster < $com");
sift-4.0.3b/web/blocks-bin/contact.pl-136-}
##############################################
sift-4.0.3b/web/blocks-bin/contact.pl-138-{
sift-4.0.3b/web/blocks-bin/contact.pl:139: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $lamamaster < $com");
sift-4.0.3b/web/blocks-bin/contact.pl-140-}
##############################################
sift-4.0.3b/web/blocks-bin/contact.pl-142-{
sift-4.0.3b/web/blocks-bin/contact.pl:143: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $webmaster < $com");
sift-4.0.3b/web/blocks-bin/contact.pl-144-}
##############################################
sift-4.0.3b/web/blocks-bin/format_blocks.pl-40- # calibrate the blocks for diy searching
sift-4.0.3b/web/blocks-bin/format_blocks.pl:41: system("$bin/calibrate.csh $blks $cblks > /dev/null");
sift-4.0.3b/web/blocks-bin/format_blocks.pl-42- # create a file of PB-weighted blocks
##############################################
sift-4.0.3b/web/blocks-bin/format_blocks.pl-44- # or other weighting schemes
sift-4.0.3b/web/blocks-bin/format_blocks.pl:45: system("$bin/blimps-bin/blweight $cblks $wblks P M > /dev/null");
sift-4.0.3b/web/blocks-bin/format_blocks.pl-46-
sift-4.0.3b/web/blocks-bin/format_blocks.pl-47- # create the PSSM files == $pssm & $mast
sift-4.0.3b/web/blocks-bin/format_blocks.pl:48: system("$bin/blimps-bin/blk2pssm $wblks $pssm B > /dev/null");
sift-4.0.3b/web/blocks-bin/format_blocks.pl:49: system("$bin/blimps-bin/blk2pssm $wblks $mast M > /dev/null");
sift-4.0.3b/web/blocks-bin/format_blocks.pl-50-
sift-4.0.3b/web/blocks-bin/format_blocks.pl-51- # create the treefile == $tree
sift-4.0.3b/web/blocks-bin/format_blocks.pl:52: system("$bin/maketree.csh $wblks > /dev/null");
sift-4.0.3b/web/blocks-bin/format_blocks.pl-53-
sift-4.0.3b/web/blocks-bin/format_blocks.pl-54- # create the map file == $map
sift-4.0.3b/web/blocks-bin/format_blocks.pl:55: system("$bin/blimps-bin/makeblockmap $wblks $map > /dev/null 2>&1");
sift-4.0.3b/web/blocks-bin/format_blocks.pl-56-
sift-4.0.3b/web/blocks-bin/format_blocks.pl-57- # remove unnecessary files
sift-4.0.3b/web/blocks-bin/format_blocks.pl:58:# system("rm $cblks");
sift-4.0.3b/web/blocks-bin/format_blocks.pl-59-}
##############################################
sift-4.0.3b/web/blocks-bin/rpsblast.pl-65-# Only the first 2 arguments are getting passed this way
sift-4.0.3b/web/blocks-bin/rpsblast.pl:66:system("$bin/rpsblast.csh $seq $db $ex $filt > $out 2>&1");
sift-4.0.3b/web/blocks-bin/rpsblast.pl-67-
sift-4.0.3b/web/blocks-bin/rpsblast.pl-68-# why doesn't umask take care of this?
sift-4.0.3b/web/blocks-bin/rpsblast.pl:69:system("chmod 660 ../tmp/$$.*");
sift-4.0.3b/web/blocks-bin/rpsblast.pl-70-
##############################################
sift-4.0.3b/web/blocks-bin/rpsblast.pl-135- $mapfile = "$tmpdir/$ac.map";
sift-4.0.3b/web/blocks-bin/rpsblast.pl:136: system("$bin/blimps-bin/getseq $ac $dir/maps.dat $mapfile > /dev/null");
sift-4.0.3b/web/blocks-bin/rpsblast.pl-137-# open(MAP, "<$dir/maps.dat");
##############################################
sift-4.0.3b/web/blocks-bin/rpsblast.pl-160- close(MAP);
sift-4.0.3b/web/blocks-bin/rpsblast.pl:161: system("rm -f $mapfile");
sift-4.0.3b/web/blocks-bin/rpsblast.pl-162- }
##############################################
sift-4.0.3b/web/blocks-bin/narrow.pl-9-$tmpdir = "../tmp/$$";
sift-4.0.3b/web/blocks-bin/narrow.pl:10:system("mkdir $tmpdir");
sift-4.0.3b/web/blocks-bin/narrow.pl-11-
##############################################
sift-4.0.3b/web/blocks-bin/narrow.pl-70-
sift-4.0.3b/web/blocks-bin/narrow.pl:71:system("$bin/narrow.csh $names{type} $fin > $err 2>&1");
sift-4.0.3b/web/blocks-bin/narrow.pl-72-
##############################################
sift-4.0.3b/web/blocks-bin/aqe.pl-27-# lockfile will wait until it can lock the file
sift-4.0.3b/web/blocks-bin/aqe.pl:28:`./lockfile $lockqueuefile`;
sift-4.0.3b/web/blocks-bin/aqe.pl-29-
##############################################
sift-4.0.3b/web/blocks-bin/test.pl-41-{
sift-4.0.3b/web/blocks-bin/test.pl:42: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $siftmaster < $com");
sift-4.0.3b/web/blocks-bin/test.pl-43-}
##############################################
sift-4.0.3b/web/blocks-bin/test.pl-46- print "$names{topic} $webmaster\n";
sift-4.0.3b/web/blocks-bin/test.pl:47: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $webmaster < $com");
sift-4.0.3b/web/blocks-bin/test.pl-48-}
##############################################
sift-4.0.3b/web/blocks-bin/process_blocks.pl-117-#print "minwidth=$minwidth maxwidth=$maxwidth\n";
sift-4.0.3b/web/blocks-bin/process_blocks.pl:118:system("$bin/blimps-bin/mablock $blin $tmp/$ID B $minwidth $maxwidth > $err 2>$err");
sift-4.0.3b/web/blocks-bin/process_blocks.pl-119-
##############################################
sift-4.0.3b/web/blocks-bin/process_blocks.pl-123- # calibrate the blocks for diy searching
sift-4.0.3b/web/blocks-bin/process_blocks.pl:124: system("$bin/calibrate.csh $blks $cblks > /dev/null");
sift-4.0.3b/web/blocks-bin/process_blocks.pl-125- # create a file of PB-weighted blocks
##############################################
sift-4.0.3b/web/blocks-bin/process_blocks.pl-127- # or other weighting schemes
sift-4.0.3b/web/blocks-bin/process_blocks.pl:128: system("$bin/blimps-bin/blweight $cblks $wblks P M > /dev/null");
sift-4.0.3b/web/blocks-bin/process_blocks.pl-129-
sift-4.0.3b/web/blocks-bin/process_blocks.pl-130- # create the PSSM files == $pssm & $mast
sift-4.0.3b/web/blocks-bin/process_blocks.pl:131: system("$bin/blimps-bin/blk2pssm $wblks $pssm B > /dev/null");
sift-4.0.3b/web/blocks-bin/process_blocks.pl:132: system("$bin/blimps-bin/blk2pssm $wblks $mast M > /dev/null");
sift-4.0.3b/web/blocks-bin/process_blocks.pl-133-
sift-4.0.3b/web/blocks-bin/process_blocks.pl-134- # create the treefile == $tree
sift-4.0.3b/web/blocks-bin/process_blocks.pl:135: system("$bin/maketree.csh $wblks > /dev/null");
sift-4.0.3b/web/blocks-bin/process_blocks.pl-136-
sift-4.0.3b/web/blocks-bin/process_blocks.pl-137- # create the map file == $map
sift-4.0.3b/web/blocks-bin/process_blocks.pl:138: system("$bin/blimps-bin/makeblockmap $wblks $map > /dev/null 2>&1");
sift-4.0.3b/web/blocks-bin/process_blocks.pl-139-
sift-4.0.3b/web/blocks-bin/process_blocks.pl-140- # remove unnecessary files
sift-4.0.3b/web/blocks-bin/process_blocks.pl:141:# system("rm $blin $blks $tmp/$ID.seqs");
sift-4.0.3b/web/blocks-bin/process_blocks.pl-142-}
##############################################
sift-4.0.3b/web/blocks-bin/impala.pl-58-# Only the first 2 arguments are getting passed this way
sift-4.0.3b/web/blocks-bin/impala.pl:59:system("$bin/impala.csh $seq $db $ex $filt > $out 2>&1");
sift-4.0.3b/web/blocks-bin/impala.pl-60-
sift-4.0.3b/web/blocks-bin/impala.pl-61-# why doesn't umask take care of this?
sift-4.0.3b/web/blocks-bin/impala.pl:62:system("chmod 660 ../tmp/$$.*");
sift-4.0.3b/web/blocks-bin/impala.pl-63-
##############################################
sift-4.0.3b/web/blocks-bin/clean.pl-12-
sift-4.0.3b/web/blocks-bin/clean.pl:13:system("ls -t ../tmp > $tmp");
sift-4.0.3b/web/blocks-bin/clean.pl-14-
##############################################
sift-4.0.3b/web/blocks-bin/clean.pl-22- if ((-T $file) && ((-M $file) > $days))
sift-4.0.3b/web/blocks-bin/clean.pl:23: { system("rm -f $file"); }
sift-4.0.3b/web/blocks-bin/clean.pl-24-# { print "$file\n"; }
##############################################
sift-4.0.3b/web/blocks-bin/clean.pl-26-close(IN);
sift-4.0.3b/web/blocks-bin/clean.pl:27:system("rm -f $tmp");
sift-4.0.3b/web/blocks-bin/clean.pl-28-exit(0);
##############################################
sift-4.0.3b/web/blocks-bin/blockmap.pl-171- $x = "'$name'";
sift-4.0.3b/web/blocks-bin/blockmap.pl:172: open(WAIS, "-|") || exec ("./waisq", "-c", $waisd, "-s", $waisd, "-m", "10", "-f", "-", "-S", "blocks.src", "-g", $x);
sift-4.0.3b/web/blocks-bin/blockmap.pl-173-
##############################################
sift-4.0.3b/web/blocks-bin/add_queue_entry.pl-17-# lockfile will wait until it can lock the file
sift-4.0.3b/web/blocks-bin/add_queue_entry.pl:18:`./lockfile $lockqueuefile`;
sift-4.0.3b/web/blocks-bin/add_queue_entry.pl-19-
##############################################
sift-4.0.3b/web/blocks-bin/contest.pl-133-{
sift-4.0.3b/web/blocks-bin/contest.pl:134: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $siftmaster < $com");
sift-4.0.3b/web/blocks-bin/contest.pl-135-}
##############################################
sift-4.0.3b/web/blocks-bin/contest.pl-137-{
sift-4.0.3b/web/blocks-bin/contest.pl:138: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $lamamaster < $com");
sift-4.0.3b/web/blocks-bin/contest.pl-139-}
##############################################
sift-4.0.3b/web/blocks-bin/contest.pl-141-{
sift-4.0.3b/web/blocks-bin/contest.pl:142: system("$mailprog -s \"comment $names{topic}\" -r $names{email} $webmaster < $com");
sift-4.0.3b/web/blocks-bin/contest.pl-143-}
##############################################
sift-4.0.3b/web/blocks-bin/makeblocks.pl-54-$ipaddr = $ENV{"REMOTE_ADDR"};
sift-4.0.3b/web/blocks-bin/makeblocks.pl:55:$nixstatus = system("./nixcheck.pl $ipaddr");
sift-4.0.3b/web/blocks-bin/makeblocks.pl-56-if ($nixstatus != 0) { exit(-1); }
##############################################
sift-4.0.3b/web/blocks-bin/makeblocks.pl-128-$id = $$;
sift-4.0.3b/web/blocks-bin/makeblocks.pl:129:system("mkdir -p $tmp/$id");
sift-4.0.3b/web/blocks-bin/makeblocks.pl:130:system("chmod -f 770 $tmp/$id");
sift-4.0.3b/web/blocks-bin/makeblocks.pl-131-$prefix = "$tmp/$id/$id";
##############################################
sift-4.0.3b/web/blocks-bin/makeblocks.pl-165-{
sift-4.0.3b/web/blocks-bin/makeblocks.pl:166: system("./add_queue_entry.pl MAKER_queue ./protomat.csh $prefix $return");
sift-4.0.3b/web/blocks-bin/makeblocks.pl-167- print "Your results will be emailed to $return\n";
##############################################
sift-4.0.3b/web/blocks-bin/makeblocks.pl-172- select(STDOUT); $| = 1;
sift-4.0.3b/web/blocks-bin/makeblocks.pl:173: system("./protomat.csh $prefix $return 2>&1 /dev/null");
sift-4.0.3b/web/blocks-bin/makeblocks.pl-174-}
##############################################
sift-4.0.3b/web/blocks-bin/codehop.pl-122-print "<PRE>";
sift-4.0.3b/web/blocks-bin/codehop.pl:123:system("$program $blocks $out '$parameters' > $err 2>&1");
sift-4.0.3b/web/blocks-bin/codehop.pl-124-open (ERR, "<$err");
##############################################
sift-4.0.3b/web/blocks-bin/codehop.pl-129-# Make sure group can remove these files
sift-4.0.3b/web/blocks-bin/codehop.pl:130:system("chmod -f 660 ../tmp/$$.*");
sift-4.0.3b/web/blocks-bin/codehop.pl:131:#system("rm $err");
sift-4.0.3b/web/blocks-bin/codehop.pl-132-#
##############################################
sift-4.0.3b/web/blocks-bin/run_queue.pl-32-if (!(-e $queuefile)) {
sift-4.0.3b/web/blocks-bin/run_queue.pl:33: `touch $queuefile`;
sift-4.0.3b/web/blocks-bin/run_queue.pl-34-}
##############################################
sift-4.0.3b/web/blocks-bin/run_queue.pl-46- $command = &readlineorsleep();
sift-4.0.3b/web/blocks-bin/run_queue.pl:47: system($command);
sift-4.0.3b/web/blocks-bin/run_queue.pl-48-}
##############################################
sift-4.0.3b/web/blocks-bin/run_queue.pl-78- # lockfile will wait until it can lock the file
sift-4.0.3b/web/blocks-bin/run_queue.pl:79: `./lockfile $lockqueuefile`;
sift-4.0.3b/web/blocks-bin/run_queue.pl-80- open(TMPFILE, ">$tmpqueuefile");
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl-121- close (CHR_FILE_NEW);
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl:122: system("mv $all_chr_file.new $all_chr_file");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl-123-}
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl-162-if ($job_size == 0){
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl:163: system("rm -f $tmp/$new_pid.chrfile");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl-164- print OUTPAGE "Complete set\t";
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl-193-close (OUTPAGE);
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl:194:#system("cp $tmp/$pid.outpage.txt $tmp/$pid.outpage.swap.txt");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl-195-#direct to the outpage url
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl-209-}
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl:210:system("$bin/sift_feed_to_chr_coords_batch.pl $tmp/$pid.batchfile $tmp $Variation_db_dir");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_nssnvs.pl-211-close (BATCH_FILE);
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-70-#check input validity and reformat chrfile
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl:71:system("perl $reformat_chrfile $all_chr_file $tmp");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-72-
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-78-#convert chrfile to gff for intersecting with small indel errors file.
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl:79:system("perl $indelfile_to_gff $all_chr_file");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-80-$all_chr_gff_file = "$all_chr_file.gff";
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-82-#Now intersect gff chrfile with small indels ref file
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl:83:system("$intersect_locations $all_chr_gff_file gff $small_indels_error_gff gff simple > $small_indels_error_intersect_file");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-84-
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-100-#Creat binned SNP files for SNP Classifier
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl:101:system("$bin/map_coords_to_bin_indels.pl $bin_file $all_chr_file $pid $tmp");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-102-#create index of old coords to new coords using pid_old_new_coords_map.txt
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-255- my $modified_seq = $elts[6];
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl:256: @indel_location_features = split /\t/, `$model_transcript $enst $indel_start $indel_stop $Variation_db_dir`;
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-257- $indel_start_CDS = $indel_location_features[0];
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-275- $outfile = "$tmp/$pid\_$enst\_$hit_id\_comparison.fasta";
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl:276: @indel_result = split /\t/, `$detect_indel $original_seq $modified_seq $outfile`;
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-277- $aa_coords_original = $indel_result[0];
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-305-my $repeat_detect_output_file = "$tmp/$pid\_repeat_detect_output_file.txt";
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl:306:system("$detect_repeat $repeat_detect_input_file $repeat_db_file > $repeat_detect_output_file");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-307-
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-804- # lockfile will wait until it can lock the file
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl:805: `./lockfile $lockqueuefile`;
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_exome_indels.pl-806-
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/Classify_SNPs_Indels.pl-821- my $stmpfile = "tmp008";
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/Classify_SNPs_Indels.pl:822: system ("echo \">query\n$query_seq\n\" > $qtmpfile");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/Classify_SNPs_Indels.pl:823: system ("echo \">subject\n$subject_seq\n\" > $stmpfile");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/Classify_SNPs_Indels.pl:824: my $result = `blast -p blastp -i $qtmpfile -j $stmpfile`; # | grep Identities | head -n 1`;
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/Classify_SNPs_Indels.pl-825-
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_intersect_cds.pl-88-
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_intersect_cds.pl:89: system ("sort -k1,1 -k4,4n -k5,5n $new_chr_file > $new_chr_file.sorted");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_intersect_cds.pl:90:my @lines_to_get = `$bin/IntersectLocations.sh $new_chr_file.sorted gff $coding_file gff simple | grep -v Total | cut -f1 | uniq`;
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/SIFT_intersect_cds.pl-91-
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/indelfile_to_gff.pl-33-close (GFFFILE);
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/indelfile_to_gff.pl:34:system ("sort -k1,1 -k4,4n -k5,5n $snpfile.journal > $snpfile.gff");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/indelfile_to_gff.pl-35-unlink("$snpfile.journal");
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/reformat_chrfile.pl-69-}
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/reformat_chrfile.pl:70:system ("mv $tempfile $chrfile");
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/sift_feed_to_chr_coords_batch.pl-27-
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/sift_feed_to_chr_coords_batch.pl:28: system ("$bin/snv_db_engine.pl $tmp $Variation_db_dir $master_pid $pid $chrfile $org $seq_identity_filter $last_partition $COORD_SYSTEM $output_options $address");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/sift_feed_to_chr_coords_batch.pl-29-}
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-73-#Creat binned SNP files for querying human chr database- the script also creates snp_chr_map_file to map bin file to chr database and table
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:74:system("$bin/map_coords_to_bin.pl $bin_file $all_chr_file $pid $tmp");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-75-
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-87- $db_chr->do('PRAGMA cache_size=4000');
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:88: #$sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD1 = ? AND COORD2 = ? ");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-89- open (BIN_FILE, "$tmp/$snp_chr_bin_file") || die ("Cannot open snp_chr_bin_file");
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-118- #}
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:119: #system("echo $snp_chr_bin_file $count >> $tmp/$pid.query_status.txt");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-120- ###
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-126- ### uncomment following block if using in operator - see above
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:127: $sth_db_chr = $db_chr->prepare("select * from $table_chr where chr = \'chr$chr\' AND COORD2 in ($coord2_str) AND COORD1 in ($coord1_str)");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:128: #system ("echo \"select * from $table_chr where chr = \'chr$chr\' AND COORD2 in \($coord2_str\) AND COORD1 in \($coord1_str\)\" > $tmp/remove");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-129- $sth_db_chr->execute();
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-133- }
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:134: system("echo $snp_chr_bin_file $count $time>> $tmp/$pid.query_status.txt");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-135- ###
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-235- $row2 = "$row\t$ensg\t$gene_name\t$gene_desc\t$ensfm\t$fam_desc\t$gene_status\t$fam_size\t$kaks_mouse\t$kaks_macaque\t$mim_status\t$freq_av\t$freq_ceu";
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:236: #system("echo $row2 >> $tmp/remove1");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-237- $key = "$chr\t$coord1\t$coord2\t$CDS\t$ensp_exists";
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-334- #print "$row<BR>";
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:335: #system("echo $row >> $tmp/remove");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-336- @elts_CDS = split /\t/, $row;
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-579-update_status($master_pid,$pid,"Complete");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:580:system("rm -f $tmp/$pid.*.siftresults.predictions");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-581-
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-688- close (OUTPAGE);
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:689: system ("chmod 755 $tmp/$master_pid.outpage.modified.txt");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-690- rename "$tmp/$master_pid.outpage.modified.txt", "$tmp/$master_pid.outpage.txt"
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-732- close (OUTPAGE);
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:733: system ("chmod 755 $tmp/$master_pid.outpage.modified.txt");
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-734- rename "$tmp/$master_pid.outpage.modified.txt", "$tmp/$master_pid.outpage.txt"
##############################################
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-1023- # lockfile will wait until it can lock the file
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl:1024: `./lockfile $lockqueuefile`;
sift-4.0.3b/.pc/fix_perl_interpreter_and_lib_path/bin/snv_db_engine.pl-1025-