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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
trnascan-se-2.0.7+ds/src/fasta2gsi.in-99-print "Sorting the intermediate index file...\n";
trnascan-se-2.0.7+ds/src/fasta2gsi.in:100:system("sort -o $tmpfile $tmpfile");
trnascan-se-2.0.7+ds/src/fasta2gsi.in-101-
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Eufind.pm-109- # run default Eufind using selected param set
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Eufind.pm:110: my $eufind_output = `$eufind_bin -i $start_index -F -I $eufind_intscore -l $max_int_len $eufind_params $tmp_fa`;
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Eufind.pm-111- if (&error_exit_status("EufindtRNA",$seq_name))
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2124- $log->broadcast($covels_cmd);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm:2125: my $covels_output = `$covels_cmd`;
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2126-
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2157- $covels_cmd = $self->covels_bin()." -w$scan_len -t$report_cutoff $$r_cur_cm_file ".$global_constants->get("tmp_trnaseq_file");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm:2158: $covels_output = `$covels_cmd`;
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2159- if ($? != 0)
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2223- $log->broadcast($coves_cmd);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm:2224: $coves_output = `$coves_cmd`;
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2225- if ($? != 0)
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2459- $log->broadcast($cms_cmd);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm:2460: system($cms_cmd);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2461-
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2519- $log->broadcast($cms_cmd);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm:2520: system($cms_cmd);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2521-
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2920- my $coves_cmd = $self->{coves_bin}." -s ".$self->{cove_cm_file_path}." ".$tmp_trnaseq_file." > ".$cove_output_file;
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm:2921: system($coves_cmd);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-2922- if ($? != 0)
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-3019-
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm:3020: @cms_lines = split(/\n/, `cat $cms_output_file`);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/CM.pm-3021- $hit_ct = 0;
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-147- # run default tRNAscan 1.4 using selected param set
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm:148: system ("$tscan_bin -i $start_index -c $tscan_params $tmp_fa > $tmp_raw");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-149- if (&error_exit_status("tRNAscan", $seq_name))
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-158- {
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm:159: system ("$tscan_bin -c $tscan_params $tmp_fa > $tmp_raw");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-160- }
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-164- {
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm:165: system ("$tscan_bin -SEQ $tmp_fa -TEMPLATE SEtemplate -OUTPUT $tmp_raw > /dev/null");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-166- }
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-172- {
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm:173: system ("ln -s ".$lib_dir."TPCsignal TPCsignal");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-174- }
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-176- {
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm:177: system ("ln -s ".$lib_dir."Dsignal Dsignal");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-178- }
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm:179: system ("reformat -ld genbank $tmp_fa > tmp.gb");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm:180: system ("$tscan_bin tmp.gb $tmp_raw > /dev/null");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-181- system ("rm tmp.gb");
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-198- close TSCANVERB;
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm:199: system ("cat tscan.verb.out >> $verb_file");
trnascan-se-2.0.7+ds/lib/tRNAscanSE/Tscan.pm-200-}
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/SprinzlAlign.pm-53- my $cmd = $cmalign_bin." -g --notrunc --dnaout ".$cm." ".$temp_fa." > ".$temp_out;
trnascan-se-2.0.7+ds/lib/tRNAscanSE/SprinzlAlign.pm:54: system($cmd);
trnascan-se-2.0.7+ds/lib/tRNAscanSE/SprinzlAlign.pm-55-
##############################################
trnascan-se-2.0.7+ds/lib/tRNAscanSE/ArrayCMscanResults.pm-186- {
trnascan-se-2.0.7+ds/lib/tRNAscanSE/ArrayCMscanResults.pm:187: $hit_overlap = eval(($self->{indexes}->[$i]->[2] eq $self->{indexes}->[$i+1]->[2]) &&
trnascan-se-2.0.7+ds/lib/tRNAscanSE/ArrayCMscanResults.pm-188- (&seg_overlap($self->{indexes}->[$i]->[3], $self->{indexes}->[$i]->[4], $self->{indexes}->[$i+1]->[3], $self->{indexes}->[$i+1]->[4], $overlap_range)));
##############################################
trnascan-se-2.0.7+ds/debian/createmanpages-4-
trnascan-se-2.0.7+ds/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
trnascan-se-2.0.7+ds/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
##############################################
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-318- # remove temporary files
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src:319: system("rm -f $tmp_raw $tmp_fa");
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-320- $seq_file->release_memory(); # release memory
##############################################
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-502-
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src:503: system("rm -f ".$global_constants->get("tmp_trnaseq_file"));
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-504-
##############################################
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-557-
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src:558: system("rm -f ".$global_constants->get("tmp_trnaseq_file"));
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-559-
##############################################
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-596-{
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src:597: system("rm -f ".$global_constants->get("temp_dir")."/tscan$$".'*');
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src:598: system("rm -f ".$opts->fafile().".pid");
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-599-}
##############################################
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-1911- {
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src:1912: system("cat $filename >> $tmp_multiseq_file");
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/tRNAscan-SE.src-1913- }
##############################################
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/EukHighConfidenceFilter.in-180-{
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/EukHighConfidenceFilter.in:181: system("mkdir -p ".$opt_output);
trnascan-se-2.0.7+ds/.pc/pkg-data.patch/EukHighConfidenceFilter.in-182- $file_names{tRNAscan_out} = $opt_result;
##############################################
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-318- # remove temporary files
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src:319: system("rm -f $tmp_raw $tmp_fa");
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-320- $seq_file->release_memory(); # release memory
##############################################
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-502-
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src:503: system("rm -f ".$global_constants->get("tmp_trnaseq_file"));
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-504-
##############################################
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-557-
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src:558: system("rm -f ".$global_constants->get("tmp_trnaseq_file"));
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-559-
##############################################
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-596-{
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src:597: system("rm -f ".$global_constants->get("temp_dir")."/tscan$$".'*');
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src:598: system("rm -f ".$opts->fafile().".pid");
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-599-}
##############################################
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-1911- {
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src:1912: system("cat $filename >> $tmp_multiseq_file");
trnascan-se-2.0.7+ds/.pc/confdir.patch/tRNAscan-SE.src-1913- }
##############################################
trnascan-se-2.0.7+ds/EukHighConfidenceFilter.in-180-{
trnascan-se-2.0.7+ds/EukHighConfidenceFilter.in:181: system("mkdir -p ".$opt_output);
trnascan-se-2.0.7+ds/EukHighConfidenceFilter.in-182- $file_names{tRNAscan_out} = $opt_result;
##############################################
trnascan-se-2.0.7+ds/tRNAscan-SE.src-318- # remove temporary files
trnascan-se-2.0.7+ds/tRNAscan-SE.src:319: system("rm -f $tmp_raw $tmp_fa");
trnascan-se-2.0.7+ds/tRNAscan-SE.src-320- $seq_file->release_memory(); # release memory
##############################################
trnascan-se-2.0.7+ds/tRNAscan-SE.src-502-
trnascan-se-2.0.7+ds/tRNAscan-SE.src:503: system("rm -f ".$global_constants->get("tmp_trnaseq_file"));
trnascan-se-2.0.7+ds/tRNAscan-SE.src-504-
##############################################
trnascan-se-2.0.7+ds/tRNAscan-SE.src-557-
trnascan-se-2.0.7+ds/tRNAscan-SE.src:558: system("rm -f ".$global_constants->get("tmp_trnaseq_file"));
trnascan-se-2.0.7+ds/tRNAscan-SE.src-559-
##############################################
trnascan-se-2.0.7+ds/tRNAscan-SE.src-596-{
trnascan-se-2.0.7+ds/tRNAscan-SE.src:597: system("rm -f ".$global_constants->get("temp_dir")."/tscan$$".'*');
trnascan-se-2.0.7+ds/tRNAscan-SE.src:598: system("rm -f ".$opts->fafile().".pid");
trnascan-se-2.0.7+ds/tRNAscan-SE.src-599-}
##############################################
trnascan-se-2.0.7+ds/tRNAscan-SE.src-1911- {
trnascan-se-2.0.7+ds/tRNAscan-SE.src:1912: system("cat $filename >> $tmp_multiseq_file");
trnascan-se-2.0.7+ds/tRNAscan-SE.src-1913- }