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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
estscan-3.0.3/extract_UG_EST-165- foreach my $id (@emblmrnas) {
estscan-3.0.3/extract_UG_EST:166: my $e = `fetch $id`;
estscan-3.0.3/extract_UG_EST-167- if (($e =~ m/^ID\s+\S+; SV \d+; linear; mRNA;/s)
##############################################
estscan-3.0.3/extract_UG_EST-209- my $matchfh = gensym;
estscan-3.0.3/extract_UG_EST:210: system("touch $matchfile");
estscan-3.0.3/extract_UG_EST-211- foreach (@clusters) {
##############################################
estscan-3.0.3/extract_UG_EST-222- # find full RNA and the position of its coding sequence
estscan-3.0.3/extract_UG_EST:223: my $e = `fetch $mrna`;
estscan-3.0.3/extract_UG_EST-224- if ($e =~ m/CDS\s+(\d+)\.\.(\d+)/) {
##############################################
estscan-3.0.3/extract_UG_EST-317- my $matchfile = "$datadir/Evaluate/matches.lst";
estscan-3.0.3/extract_UG_EST:318: my $nbMatches = `wc -l $matchfile`;
estscan-3.0.3/extract_UG_EST-319- $nbMatches =~ m/^\s*(\S+)/;
##############################################
estscan-3.0.3/build_model_utils.pl-59- }
estscan-3.0.3/build_model_utils.pl:60: if (!eval `cat $parFileName`) { die "Error in '$parFileName': $@"; }
estscan-3.0.3/build_model_utils.pl-61- if (!defined($organism)) { die '$organism not specified in '.$parFileName; }
##############################################
estscan-3.0.3/prepare_data-372- log_print(" - masking redundancy in isochore $isochore");
estscan-3.0.3/prepare_data:373: system("maskred -m $minmask < $infile > $maskedFile");
estscan-3.0.3/prepare_data-374- }
estscan-3.0.3/prepare_data:375: my $masked = `tail -1 $maskedFile`;
estscan-3.0.3/prepare_data-376- $masked =~ m/^>masked nucleotides: (\d+)/;
estscan-3.0.3/prepare_data-377- my $m = $1;
estscan-3.0.3/prepare_data:378: my $nts = `grep -v '^>' $maskedFile | wc -cl`;
estscan-3.0.3/prepare_data-379- $nts =~ s/^\s*(\d+)\s+(\d+)\s*$/$2-$1/e;
##############################################
estscan-3.0.3/prepare_data-421-
estscan-3.0.3/prepare_data:422: my $nbUTRs = `grep -c '^>' $utrfile`; chop($nbUTRs);
estscan-3.0.3/prepare_data:423: my $nbCDSs = `grep -c '^>' $cdsfile`; chop($nbCDSs);
estscan-3.0.3/prepare_data-424- log_print(" found $nbUTRs untranslated regions and $nbCDSs coding sequences");
##############################################
estscan-3.0.3/build_model-162- " < $isodir/mrna$iso";
estscan-3.0.3/build_model:163: my $out = `$cmd`;
estscan-3.0.3/build_model-164- $out =~ s/<NAME>/$parFile/g;
##############################################
estscan-3.0.3/evaluate_model-116- $nb_isochores, $isochore_borders);
estscan-3.0.3/evaluate_model:117: if (system("which $program") != 0) {
estscan-3.0.3/evaluate_model-118- log_print(" fatal: $program not found");
##############################################
estscan-3.0.3/evaluate_model-171- my ($prefix, $cdsutr, $estfile, $smatfile, $estscanparams) = @_;
estscan-3.0.3/evaluate_model:172: my $x = `grep -i '^[a-z]' $estfile | wc`;
estscan-3.0.3/evaluate_model-173- $x =~ s/^\s+//;
##############################################
estscan-3.0.3/evaluate_model-187- }
estscan-3.0.3/evaluate_model:188: $x = `grep -i '^[a-z]' $prcfile | wc`;
estscan-3.0.3/evaluate_model-189- $x =~ s/^\s+//;
##############################################
estscan-3.0.3/evaluate_model-192- my $r = $nbPrc/$nbTot;
estscan-3.0.3/evaluate_model:193: my $nbSeq = `grep -c '^>' $prcfile`;
estscan-3.0.3/evaluate_model-194- chop $nbSeq;
estscan-3.0.3/evaluate_model:195: my $nbTotSeq = `grep -c '^>' $estfile`;
estscan-3.0.3/evaluate_model-196- chop $nbTotSeq;
##############################################
estscan-3.0.3/evaluate_model-321- my $utrfile = "$datadir/Evaluate/estutr.seq";
estscan-3.0.3/evaluate_model:322: my $x = `grep -i '^[a-z]' $utrfile | wc`;
estscan-3.0.3/evaluate_model-323- $x =~ s/^\s+//;
##############################################
estscan-3.0.3/evaluate_model-326- $utrfile = "$datadir/Evaluate/$prefix" . "prc$filestem$EP" . "_utr.seq";
estscan-3.0.3/evaluate_model:327: $x = `grep -i '^[a-z]' $utrfile | wc`;
estscan-3.0.3/evaluate_model-328- $x =~ s/^\s+//;
##############################################
estscan-3.0.3/extract_EST-213- log_print(" - matching coding sequences ($cdsfile) against ESTs...");
estscan-3.0.3/extract_EST:214: system("cd $datadir/Evaluate; megablast -d estdb -i $cdsfile > $cdsvsestfile");
estscan-3.0.3/extract_EST-215- }
##############################################
estscan-3.0.3/extract_EST-222- log_print(" $matchedFile already exists, skipped.");
estscan-3.0.3/extract_EST:223: $nbMatched = `grep -c '>' $matchedFile`; chop($nbMatched);
estscan-3.0.3/extract_EST-224- }
##############################################
estscan-3.0.3/extract_EST-261- log_print(" - predicting CDS for matched ESTs...");
estscan-3.0.3/extract_EST:262: system("$program $estscanparams -M $smatfile $matchedFile > $prcfile");
estscan-3.0.3/extract_EST-263- }
estscan-3.0.3/extract_EST:264: my $nbPrc = `grep -c '>' $prcfile`; chop($nbPrc);
estscan-3.0.3/extract_EST-265- log_print(" found $nbPrc predicted coding sequences");
##############################################
estscan-3.0.3/extract_EST-327- log_print(" shuffling EST-data...");
estscan-3.0.3/extract_EST:328: system("winsegshuffle 500000 $length < $estfile > $shuffledFile");
estscan-3.0.3/extract_EST-329- }
estscan-3.0.3/extract_EST:330: my $nbShuffled = `grep -c '>' $shuffledFile`; chop($nbShuffled);
estscan-3.0.3/extract_EST-331- $totalShuffled += $nbShuffled;
##############################################
estscan-3.0.3/extract_EST-341- log_print(" predicting coding on shuffled files...");
estscan-3.0.3/extract_EST:342: system("$program $estscanparams -M $smatfile $shuffledFile > $prcfile");
estscan-3.0.3/extract_EST-343- }
estscan-3.0.3/extract_EST:344: my $nbPrc = `grep -c '>' $prcfile`; chop($nbPrc);
estscan-3.0.3/extract_EST-345- log_print(" estimated false positive rate: " .
##############################################
estscan-3.0.3/extract_mRNA-106- $fileLen = 0;
estscan-3.0.3/extract_mRNA:107: $_ = `head -1 $file`;
estscan-3.0.3/extract_mRNA-108- if (m/^LOCUS/) { # we read a file in genbank format