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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
transdecoder-5.0.1/PerlLib/Pipeliner.pm-39- print STDERR "CMD: $cmd\n";
transdecoder-5.0.1/PerlLib/Pipeliner.pm:40: my $ret = system($cmd);
transdecoder-5.0.1/PerlLib/Pipeliner.pm-41- if ($ret) {
##############################################
transdecoder-5.0.1/PerlLib/Pipeliner.pm-157-
transdecoder-5.0.1/PerlLib/Pipeliner.pm:158: my $ret = system($cmdstr);
transdecoder-5.0.1/PerlLib/Pipeliner.pm-159- if ($ret) {
##############################################
transdecoder-5.0.1/PerlLib/Pipeliner.pm-161- if (-e $tmp_stderr) {
transdecoder-5.0.1/PerlLib/Pipeliner.pm:162: system("cat $tmp_stderr");
transdecoder-5.0.1/PerlLib/Pipeliner.pm-163- unlink($tmp_stderr);
##############################################
transdecoder-5.0.1/PerlLib/Pipeliner.pm-168- else {
transdecoder-5.0.1/PerlLib/Pipeliner.pm:169: `touch $checkpoint_file`;
transdecoder-5.0.1/PerlLib/Pipeliner.pm-170- if ($?) {
##############################################
transdecoder-5.0.1/PerlLib/Process_cmd.pm-17-
transdecoder-5.0.1/PerlLib/Process_cmd.pm:18: my $ret = system($cmd);
transdecoder-5.0.1/PerlLib/Process_cmd.pm-19- if ($ret) {
##############################################
transdecoder-5.0.1/util/PWM/compute_AUC.pl-81-
transdecoder-5.0.1/util/PWM/compute_AUC.pl:82: system("Rscript $Rscript_file");
transdecoder-5.0.1/util/PWM/compute_AUC.pl-83-
##############################################
transdecoder-5.0.1/util/extract_FL_subset.pl-124- print "CMD: $cmd\n";
transdecoder-5.0.1/util/extract_FL_subset.pl:125: my $ret = system($cmd);
transdecoder-5.0.1/util/extract_FL_subset.pl-126-
##############################################
transdecoder-5.0.1/util/ffindex_resume.pl-47- unlink($input_idx.".notdone");
transdecoder-5.0.1/util/ffindex_resume.pl:48: system("cat $done_input | tr -d '\000' > $done_input.txt");
transdecoder-5.0.1/util/ffindex_resume.pl-49- exit;
##############################################
transdecoder-5.0.1/util/pfam_runner.pl-188- print "CMD: $cmd\n";
transdecoder-5.0.1/util/pfam_runner.pl:189: my $ret = system($cmd);
transdecoder-5.0.1/util/pfam_runner.pl-190-
##############################################
transdecoder-5.0.1/util/pfam_runner.pl-202- &process_cmd("$UTIL_DIR/bin/ffindex_from_fasta -s $fasta_file.db $fasta_file.db.idx $fasta_file") unless -s "$fasta_file.db";
transdecoder-5.0.1/util/pfam_runner.pl:203: my $sequence_number = `wc -l < $fasta_file.db.idx`;
transdecoder-5.0.1/util/pfam_runner.pl-204- chomp($sequence_number);
##############################################
transdecoder-5.0.1/util/pfam_runner.pl-251- my $transcript_db = shift;
transdecoder-5.0.1/util/pfam_runner.pl:252: my $number_of_peps = `grep '>' $transcript_db | wc -l `;
transdecoder-5.0.1/util/pfam_runner.pl-253- chomp $number_of_peps;
##############################################
transdecoder-5.0.1/util/pfam_runner.pl-300- foreach my $prog (@_) {
transdecoder-5.0.1/util/pfam_runner.pl:301: my $path = `which $prog`;
transdecoder-5.0.1/util/pfam_runner.pl-302- die "Error, path to a required program ($prog) cannot be found\n\n"
##############################################
transdecoder-5.0.1/debian/createmanpages-4-
transdecoder-5.0.1/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
transdecoder-5.0.1/debian/createmanpages-6-
##############################################
transdecoder-5.0.1/debian/tests/run-tests-4-if [ "$ADTTMP" = "" ] ; then
transdecoder-5.0.1/debian/tests/run-tests:5: ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
transdecoder-5.0.1/debian/tests/run-tests-6-fi
##############################################
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.LongOrfs-173-
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.LongOrfs:174: my $num_total_trans = `grep '>' $transcripts_file | wc -l`;
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.LongOrfs-175- chomp $num_total_trans;
##############################################
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.LongOrfs-346- print "CMD: $cmd\n";
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.LongOrfs:347: my $ret = system($cmd);
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.LongOrfs-348-
##############################################
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.Predict-357- print "CMD: $cmd\n";
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.Predict:358: my $ret = system($cmd);
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.Predict-359-
##############################################
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.Predict-424- foreach my $prog (@_) {
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.Predict:425: my $path = `which $prog`;
transdecoder-5.0.1/.pc/fix-whatis/TransDecoder.Predict-426- unless ($path =~ /\w/) {
##############################################
transdecoder-5.0.1/TransDecoder.LongOrfs-173-
transdecoder-5.0.1/TransDecoder.LongOrfs:174: my $num_total_trans = `grep '>' $transcripts_file | wc -l`;
transdecoder-5.0.1/TransDecoder.LongOrfs-175- chomp $num_total_trans;
##############################################
transdecoder-5.0.1/TransDecoder.LongOrfs-346- print "CMD: $cmd\n";
transdecoder-5.0.1/TransDecoder.LongOrfs:347: my $ret = system($cmd);
transdecoder-5.0.1/TransDecoder.LongOrfs-348-
##############################################
transdecoder-5.0.1/TransDecoder.Predict-357- print "CMD: $cmd\n";
transdecoder-5.0.1/TransDecoder.Predict:358: my $ret = system($cmd);
transdecoder-5.0.1/TransDecoder.Predict-359-
##############################################
transdecoder-5.0.1/TransDecoder.Predict-424- foreach my $prog (@_) {
transdecoder-5.0.1/TransDecoder.Predict:425: my $path = `which $prog`;
transdecoder-5.0.1/TransDecoder.Predict-426- unless ($path =~ /\w/) {