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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
fasta3-36.3.8h.2020-02-11/README.md-66-Various bugs in sub-alignment scoring corrected and support for the
fasta3-36.3.8h.2020-02-11/README.md:67:EBI SP:GSTM1_HUMAN P09488 added. The format for the `$SRCH_URL` and
fasta3-36.3.8h.2020-02-11/README.md:68:`$SRCH_URL2` format strings has changed to enable pairwise alignment.
fasta3-36.3.8h.2020-02-11/README.md-69-
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/README.md-78-of these programs is defined in the `psisearch2_msa.pl` and
fasta3-36.3.8h.2020-02-11/psisearch2/README.md:79:`psisearch2_msa.py` scripts using the `$pgm_bin` and `$pgm_data`
fasta3-36.3.8h.2020-02-11/psisearch2/README.md-80-variable (perl, `pgm_bin` and `pgm_data` for python). You will
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-191- unless ($use_stdout) {
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:192: log_system("$search > $this_file_out 2> $this_file_out.err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-193- }
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-194- else {
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:195: log_system("$search 2> $this_file_out.err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-196- }
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-207- unless ($use_stdout) {
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:208: log_system("$search > $this_file_out 2> $this_file_out.err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-209- }
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-210- else {
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:211: log_system("$search 2> $this_file_out.err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-212- }
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-239- unless ($use_stdout) {
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:240: log_system("$search > $this_file_out 2> $this_file_out.err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-241- }
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-242- else {
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:243: log_system("$search 2> $this_file_out.err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-244- }
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-256- }
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:257: log_system("rm $prev_bound") if ($delete_bnd);
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-258-
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-269-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:270:log_system("rm $prev_bound") if ($delete_bnd);
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-271-unless ($quiet) {
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-283- print STDERR "# $cmd\n" if $error_log;
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:284: system($cmd);
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-285-}
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-384-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:385: log_system("$aln2msa_cmd $this_file_out > $this_msa");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-386-
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-388-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:389: log_system($makeblastdb_cmd);
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-390-
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-392-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:393: log_system("$buildpssm_cmd > $this_psibl_out 2> $this_psibl_out.err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-394-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:395: log_system("rm $this_hit_db.p* $blastdb_err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-396-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-397- # remove uninformative error logs
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:398: log_system("rm $this_psibl_out.err") unless $error_log;
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-399-
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-401- my $asn2asn_cmd = "$datatool_bin -v $this_pssm_asntxt -e $this_pssm_asnbin";
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:402: log_system($asn2asn_cmd);
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-403- return ($this_pssm_asnbin, $this_bound_out);
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-435-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:436: log_system($clus2fa_cmd);
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-437-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-438- my $makeblastdb_cmd = "$makeblastdb_bin -in $this_hit_db -dbtype prot -parse_seqids > $blastdb_err";
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:439: log_system($makeblastdb_cmd);
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-440-
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-442-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:443: log_system("$buildpssm_cmd > $this_psibl_out 2> $this_psibl_out.err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-444-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:445: log_system("rm $this_hit_db.p* $blastdb_err");
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-446-
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-447- # remove uninformative error logs
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:448: log_system("rm $this_psibl_out.err") unless $error_log;
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-449-
##############################################
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-451- my $asn2asn_cmd = "$datatool_bin -v $this_pssm_asntxt -e $this_pssm_asnbin";
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl:452: log_system($asn2asn_cmd);
fasta3-36.3.8h.2020-02-11/psisearch2/psisearch2_msa.pl-453- return ($this_pssm_asnbin);
##############################################
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr.pl-143-
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr.pl:144:my $get_ipr_domdb_id = $dbh->prepare(qq(select acc, start, stop, ipr_acc, db_ref, s_descr, len from prot2ipr join $a_table using(acc) join ipr_annot using(ipr_acc) where dom_db='$dom_db' AND id=? order by start));
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr.pl-145-
##############################################
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr.pl-149-
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr.pl:150:my $get_ipr_domdb_acc = $dbh->prepare(qq(select acc, start, stop, ipr_acc, db_ref, s_descr, len from prot2ipr join $a_table using(acc) join ipr_annot using(ipr_acc) where dom_db='$dom_db' AND acc=? order by start));
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr.pl-151-
##############################################
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr_e.pl-159-
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr_e.pl:160:my $get_ipr_domdb_id = $dbh->prepare(qq(select acc, start, stop, ipr_acc, db_ref, s_descr, len from prot2ipr join $a_table using(acc) join ipr_annot using(ipr_acc) where dom_db='$dom_db' AND id=? order by start));
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr_e.pl-161-
##############################################
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr_e.pl-165-
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr_e.pl:166:my $get_ipr_domdb_acc = $dbh->prepare(qq(select acc, start, stop, ipr_acc, db_ref, s_descr, len from prot2ipr join $a_table using(acc) join ipr_annot using(ipr_acc) where dom_db='$dom_db' AND acc=? order by start));
fasta3-36.3.8h.2020-02-11/scripts/ann_feats2ipr_e.pl-167-
##############################################
fasta3-36.3.8h.2020-02-11/scripts/fasta_annot_cmd.sh-78-if [ ! -s $blr_out ]; then
fasta3-36.3.8h.2020-02-11/scripts/fasta_annot_cmd.sh:79: # echo "# " `ls -l $blt_out $blr_out`
fasta3-36.3.8h.2020-02-11/scripts/fasta_annot_cmd.sh-80- blr_out=$blt_out
fasta3-36.3.8h.2020-02-11/scripts/fasta_annot_cmd.sh:81: # echo "# " `ls -l $blt_out $blr_out`
fasta3-36.3.8h.2020-02-11/scripts/fasta_annot_cmd.sh-82-fi
##############################################
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts-252- if [ ! -s $blr_out ]; then
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts:253: # echo "# " `ls -l $blt_out $blr_out`
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts-254-@@ -81,4 +81,4 @@
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts:255: # echo "# " `ls -l $blt_out $blr_out`
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts-256- fi
##############################################
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts-527-
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts:528:-for script in `cat $script_file `; do
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts:529:- for acc_type in `cat $ex_file`; do
fasta3-36.3.8h.2020-02-11/debian/patches/adjust-scripts-530-- echo $script ${acc_type}
##############################################
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr.pl-143-
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr.pl:144:my $get_ipr_domdb_id = $dbh->prepare(qq(select acc, start, stop, ipr_acc, db_ref, s_descr, len from prot2ipr join $a_table using(acc) join ipr_annot using(ipr_acc) where dom_db='$dom_db' AND id=? order by start));
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr.pl-145-
##############################################
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr.pl-149-
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr.pl:150:my $get_ipr_domdb_acc = $dbh->prepare(qq(select acc, start, stop, ipr_acc, db_ref, s_descr, len from prot2ipr join $a_table using(acc) join ipr_annot using(ipr_acc) where dom_db='$dom_db' AND acc=? order by start));
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr.pl-151-
##############################################
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr_e.pl-159-
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr_e.pl:160:my $get_ipr_domdb_id = $dbh->prepare(qq(select acc, start, stop, ipr_acc, db_ref, s_descr, len from prot2ipr join $a_table using(acc) join ipr_annot using(ipr_acc) where dom_db='$dom_db' AND id=? order by start));
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr_e.pl-161-
##############################################
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr_e.pl-165-
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr_e.pl:166:my $get_ipr_domdb_acc = $dbh->prepare(qq(select acc, start, stop, ipr_acc, db_ref, s_descr, len from prot2ipr join $a_table using(acc) join ipr_annot using(ipr_acc) where dom_db='$dom_db' AND acc=? order by start));
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/ann_feats2ipr_e.pl-167-
##############################################
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/fasta_annot_cmd.sh-78-if [ ! -s $blr_out ]; then
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/fasta_annot_cmd.sh:79: # echo "# " `ls -l $blt_out $blr_out`
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/fasta_annot_cmd.sh-80- blr_out=$blt_out
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/fasta_annot_cmd.sh:81: # echo "# " `ls -l $blt_out $blr_out`
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/fasta_annot_cmd.sh-82-fi
##############################################
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/test_ann_scripts.sh-23-
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/test_ann_scripts.sh:24:for script in `cat $script_file `; do
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/test_ann_scripts.sh:25: for acc_type in `cat $ex_file`; do
fasta3-36.3.8h.2020-02-11/.pc/adjust-scripts/scripts/test_ann_scripts.sh-26- echo $script ${acc_type}