===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
murasaki-1.68.6/repeatviz.pl-76-our $seqCount=scalar(@seqs);
murasaki-1.68.6/repeatviz.pl:77:our @seqLengths=map {my $l=`$geneparse -l $_`;chomp $l; $l} @seqs;
murasaki-1.68.6/repeatviz.pl-78-
##############################################
murasaki-1.68.6/names2kog.pl-67- my $newf="$file.cds";
murasaki-1.68.6/names2kog.pl:68: system("$root/getcds.pl $file") unless -f $newf;
murasaki-1.68.6/names2kog.pl-69- $file=$newf;
##############################################
murasaki-1.68.6/simplegraph.pl-146- print "**********************************************\n";
murasaki-1.68.6/simplegraph.pl:147: system("gnuplot $plotfile -");
murasaki-1.68.6/simplegraph.pl-148- }else{
##############################################
murasaki-1.68.6/simplegraph.pl-157-ENDTEXT
murasaki-1.68.6/simplegraph.pl:158: system("gnuplot $ffile $plotfile");
murasaki-1.68.6/simplegraph.pl-159- unlink($plotfile) unless $keepGnuplot;
murasaki-1.68.6/simplegraph.pl-160- if ($ext eq 'pdf') {
murasaki-1.68.6/simplegraph.pl:161: system("ps2pdf $outf $out_prefix.$m.pdf");
murasaki-1.68.6/simplegraph.pl:162: system("rm $outf") if -e "$out_prefix.$m.pdf" and !$useFormats{ps};
murasaki-1.68.6/simplegraph.pl-163- }
##############################################
murasaki-1.68.6/simplegraph.pl-410- return undef unless $real and -f $real;
murasaki-1.68.6/simplegraph.pl:411: my $length=`$geneparser -l $real`;
murasaki-1.68.6/simplegraph.pl-412- chomp $length;
##############################################
murasaki-1.68.6/overlay.pl-58-print "Merging using $mode\n";
murasaki-1.68.6/overlay.pl:59:system($cmd);
murasaki-1.68.6/overlay.pl-60-
##############################################
murasaki-1.68.6/getgene.pl-49- print "CDS file not found for $filename. Generating...\n";
murasaki-1.68.6/getgene.pl:50: my $res=system("$root/getcds.pl $filename");
murasaki-1.68.6/getgene.pl-51- do {
##############################################
murasaki-1.68.6/getgene.pl-70-print "Loading $filename...\n";
murasaki-1.68.6/getgene.pl:71:my $genome=`$root/geneparse.pl $filename`;
murasaki-1.68.6/getgene.pl-72-while(@ARGV){
##############################################
murasaki-1.68.6/kogalign.pl-118- print "CDS file not found for $seq. Generating...\n";
murasaki-1.68.6/kogalign.pl:119: my $res=system("$root/getcds.pl $seq");
murasaki-1.68.6/kogalign.pl-120- do {
##############################################
murasaki-1.68.6/roc-at-cutoff.pl-234- close($R);
murasaki-1.68.6/roc-at-cutoff.pl:235: system("R --vanilla < $rsrc");
murasaki-1.68.6/roc-at-cutoff.pl-236- }
##############################################
murasaki-1.68.6/dna2binary.pl-35-if($filename and -e $filename){
murasaki-1.68.6/dna2binary.pl:36: $inseq=`$root/geneparse.pl -c $filename`;
murasaki-1.68.6/dna2binary.pl-37- my ($basename,$path,$suffix) = fileparse($filename);
##############################################
murasaki-1.68.6/antisense.pl-36-if($filename and -e $filename){
murasaki-1.68.6/antisense.pl:37: $inseq=`$root/geneparse.pl -c $filename`;
murasaki-1.68.6/antisense.pl-38- my ($basename,$path,$suffix) = fileparse($filename);
##############################################
murasaki-1.68.6/cgr-image.pl-248- print "Erasing temporary PGM file.\n";
murasaki-1.68.6/cgr-image.pl:249: system("rm $filename.pgm");
murasaki-1.68.6/cgr-image.pl-250-}
##############################################
murasaki-1.68.6/align2kog.pl-90- print "Making CDS for $file...\n";
murasaki-1.68.6/align2kog.pl:91: system("$root/getcds.pl --redirect murasaki_synth=$inf $file");
murasaki-1.68.6/align2kog.pl-92- }
##############################################
murasaki-1.68.6/dnashuffle.pl-36-if($filename and -e $filename){
murasaki-1.68.6/dnashuffle.pl:37: $inseq=`$root/geneparse.pl -c $filename`;
murasaki-1.68.6/dnashuffle.pl-38- my ($basename,$path,$suffix) = fileparse($filename);
##############################################
murasaki-1.68.6/histocomp.pl-150-close($R);
murasaki-1.68.6/histocomp.pl:151:system("R --vanilla < $rsrc");
murasaki-1.68.6/histocomp.pl-152-
##############################################
murasaki-1.68.6/interpolate.pl-55- unless($maxSize>0){
murasaki-1.68.6/interpolate.pl:56: $maxSize=int(min(map {`$geneparse -l -c $_`/1000} @seqs));
murasaki-1.68.6/interpolate.pl-57- print "MaxSize set automatically to $maxSize";
##############################################
murasaki-1.68.6/mfasplit.pl-30- my ($name,$path,$suffix) = fileparse($file, qr{\.[^.]*$});
murasaki-1.68.6/mfasplit.pl:31: system("mkdir $name") unless -d $name;
murasaki-1.68.6/mfasplit.pl-32- open(INF,"<$file");
##############################################
murasaki-1.68.6/geneparse.pl-116- }else{
murasaki-1.68.6/geneparse.pl:117: print OUTF `$cmd`;
murasaki-1.68.6/geneparse.pl-118- print OUTF join('n' x 10,@parts) if $filei!=$#files;
##############################################
murasaki-1.68.6/geneparse.pl-226- }
murasaki-1.68.6/geneparse.pl:227: $lines=`wc $filename -l`;
murasaki-1.68.6/geneparse.pl-228- $len=length($line2)*($lines-2)+length($lastline);;
##############################################
murasaki-1.68.6/perlmodules/Murasaki.pm-33- my $runby=$0;
murasaki-1.68.6/perlmodules/Murasaki.pm:34: $runby=`which $runby` unless $runby=~m!/!; #unless absolute path, grab real path this way. unpleasant hack. open to suggestions.
murasaki-1.68.6/perlmodules/Murasaki.pm-35- $root=(fileparse($runby))[1];
##############################################
murasaki-1.68.6/stat-vs-stat.pl-165- close($R);
murasaki-1.68.6/stat-vs-stat.pl:166: system("R --vanilla < $rsrc");
murasaki-1.68.6/stat-vs-stat.pl-167- }
##############################################
murasaki-1.68.6/stat-histo.pl-197- close($R);
murasaki-1.68.6/stat-histo.pl:198: system("R --vanilla < $rsrc");
murasaki-1.68.6/stat-histo.pl-199-}
##############################################
murasaki-1.68.6/gatherstats.pl-205- return unless -f $fn;
murasaki-1.68.6/gatherstats.pl:206: $sizeCache{$fn}=`$root/geneparse.pl -lfc $fn`;
murasaki-1.68.6/gatherstats.pl-207- return $sizeCache{$fn};
##############################################
murasaki-1.68.6/getcds.pl-98- $runopts.=join(" ",map {"--redirect=$_"} @instantRedirects);
murasaki-1.68.6/getcds.pl:99: system("$root/getcds.pl $runopts $src") unless -f "$src.cds";
murasaki-1.68.6/getcds.pl-100- die "Couldn't load annotation data for $src" unless -f "$src.cds";
##############################################
murasaki-1.68.6/getcds.pl-223- my $dbh=getDb('ensembl',$build);
murasaki-1.68.6/getcds.pl:224: my $sth = $dbh->prepare("SELECT i.stable_id,s.name,g.seq_region_start,g.seq_region_end,g.seq_region_strand FROM gene g, gene_stable_id i, seq_region s, coord_system c WHERE c.coord_system_id=s.coord_system_id AND c.name='chromosome' AND g.gene_id=i.gene_id and s.seq_region_id=g.seq_region_id AND s.name='$chromosome'"); #weee for ugly long SQL!
murasaki-1.68.6/getcds.pl-225- print "Connected. Running query for chromosome $chromosome...\n";
##############################################
murasaki-1.68.6/getcds.pl-257-
murasaki-1.68.6/getcds.pl:258: my $length=`$root/geneparse -l -c $filename`;
murasaki-1.68.6/getcds.pl-259-
##############################################
murasaki-1.68.6/getcds.pl-351- my $dbh=getDb('ucsc',$build);
murasaki-1.68.6/getcds.pl:352: my $sth = $dbh->prepare("SELECT name,chrom,cdsStart,cdsEnd,strand FROM ensGene WHERE chrom='$chromosome'"); #weee for short boring SQL!
murasaki-1.68.6/getcds.pl-353- print "Connected. Running query for chromosome $chromosome...\n";
##############################################
murasaki-1.68.6/getcds.pl-582- print "Extracting subsequence meta-data from $filename\n";
murasaki-1.68.6/getcds.pl:583: system("$root/getsegments $filename") and die "Error creating segment data for $filename"
murasaki-1.68.6/getcds.pl-584- }
##############################################
murasaki-1.68.6/osfinder2anchors.pl-115- unless(-f "$file.len"){
murasaki-1.68.6/osfinder2anchors.pl:116: system("$root/getsegments $file");
murasaki-1.68.6/osfinder2anchors.pl-117- }
##############################################
murasaki-1.68.6/anchors2maf.pl-52-die "Lack of sequences?" unless @seqs;
murasaki-1.68.6/anchors2maf.pl:53:my %lengths=map {$_=>`$root/geneparse -l -c $_`} @seqs;
murasaki-1.68.6/anchors2maf.pl-54-
##############################################
murasaki-1.68.6/anchors2maf.pl-85- my $extract="$root/geneparse -c $seqs[$i]\[$anchor->{start},$anchor->{stop}\]";
murasaki-1.68.6/anchors2maf.pl:86: my $content=$anchor->{strand} eq '+' ? `$extract`:`$extract | $root/antisense.pl -c`;
murasaki-1.68.6/anchors2maf.pl-87- print $outfh sprintf("s %-10s %9d %4d %1s %9d ",$seqs[$i],$start,$anchor->{length},$anchor->{strand},$length).$content;
##############################################
murasaki-1.68.6/analyze-pat.pl-56- if($inf=~m/^\[\d+\D\d+\]/){
murasaki-1.68.6/analyze-pat.pl:57: $pat=`$root/randpat.pl -c $inf`;
murasaki-1.68.6/analyze-pat.pl-58- analyzePat($pat);
##############################################
murasaki-1.68.6/homology-score.pl-72- print "Loading $seq...\n";
murasaki-1.68.6/homology-score.pl:73: $seqdata{$seq}=`$root/geneparse.pl -c $seq`;
murasaki-1.68.6/homology-score.pl-74-}
##############################################
murasaki-1.68.6/homology-score.pl-129- if($aligner eq 'clustalw'){
murasaki-1.68.6/homology-score.pl:130: my $res=`$aligners{$aligner} -infile=$tmpfile -tree`;
murasaki-1.68.6/homology-score.pl-131- $res=~m/Phylogenetic tree file created:\s+\[(.+)\]/m or die "Uh oh, aligner puked:\n$res";
##############################################
murasaki-1.68.6/homology-score.pl-135- my $cmd="$aligners{$aligner} -in $tmpfile -quiet -tree1 $tmpfile.tree1 -tree2 $tmpfile.tree2 -maxiters 2";
murasaki-1.68.6/homology-score.pl:136: my $res=`$cmd`;
murasaki-1.68.6/homology-score.pl-137- my $useTree="$tmpfile.tree2";
##############################################
murasaki-1.68.6/homology-score.pl-145- parseTree(\%res,0,@treeDat);
murasaki-1.68.6/homology-score.pl:146: system("rm $tmpbase*"); #cleanup
murasaki-1.68.6/homology-score.pl-147- return %res;
##############################################
murasaki-1.68.6/anchors2osfinder.pl-63- print STDERR "Warning: Overwriting $outf\n" if -f $outf;
murasaki-1.68.6/anchors2osfinder.pl:64: my ($lines)=`wc -l $inf`=~m/(\d+)/ if -f $inf;
murasaki-1.68.6/anchors2osfinder.pl-65- resetTick($lines) if $lines;
##############################################
murasaki-1.68.6/anchors2osfinder.pl-159- unless(-f "$file.len"){
murasaki-1.68.6/anchors2osfinder.pl:160: system("$root/getsegments $file");
murasaki-1.68.6/anchors2osfinder.pl-161- }
##############################################
murasaki-1.68.6/src/openhash.cc-66-word OpenHash::sizeAt(const HashKey key,const HashVal &val){
murasaki-1.68.6/src/openhash.cc:67: return fasta[findAddr(key,val)].getSize();
murasaki-1.68.6/src/openhash.cc-68-}
##############################################
murasaki-1.68.6/src/openhash.cc-70-void OpenHash::add(const HashKey key,const HashVal &val){
murasaki-1.68.6/src/openhash.cc:71: fasta[findAddr(key,val)].push(val.seqno,val.pos);
murasaki-1.68.6/src/openhash.cc-72-}
##############################################
murasaki-1.68.6/src/openhash.cc-99-
murasaki-1.68.6/src/openhash.cc:100:HashKey OpenHash::findAddr(const HashKey start, const HashVal &val){
murasaki-1.68.6/src/openhash.cc-101-#ifdef HASHPROFILE
##############################################
murasaki-1.68.6/src/openhash.h-75- Ecolist *fasta;
murasaki-1.68.6/src/openhash.h:76: HashKey findAddr(const HashKey start,const HashVal &val);
murasaki-1.68.6/src/openhash.h-77- HashKey keysFree,keysFreeWarning;
##############################################
murasaki-1.68.6/debian-tests-data/NZ_GG705063.gbk-1604- imbedded in a TRX fold. They function as protein disulfide
murasaki-1.68.6/debian-tests-data/NZ_GG705063.gbk:1605: isomerases and chaperones in the bacterial periplasm to
murasaki-1.68.6/debian-tests-data/NZ_GG705063.gbk-1606- correct non-native disulfide bonds...; Region:
##############################################
murasaki-1.68.6/debian-tests-data/NZ_GG705069.gbk-554- imbedded in a TRX fold. They function as protein disulfide
murasaki-1.68.6/debian-tests-data/NZ_GG705069.gbk:555: isomerases and chaperones in the bacterial periplasm to
murasaki-1.68.6/debian-tests-data/NZ_GG705069.gbk-556- correct non-native disulfide bonds...; Region:
##############################################
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk-4470- and NarB catalyze the reduction of nitrate to nitrite.
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk:4471: Monomeric Nas is located in the cytoplasm and participates
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk-4472- in nitrogen assimilation. Dimeric Nap is located in the
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk:4473: periplasm and is coupled to quinol...; Region:
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk-4474- MopB_Nitrate-R-NapA-like; cd02754"
##############################################
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk-4499- and NarB catalyze the reduction of nitrate to nitrite.
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk:4500: Monomeric Nas is located in the cytoplasm and participates
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk-4501- in nitrogen assimilation. Dimeric Nap is located in the
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk:4502: periplasm and is coupled to quinol...; Region:
murasaki-1.68.6/debian-tests-data/NZ_GG705060.gbk-4503- MopB_CT_Nitrate-R-NapA-like; cd02791"
##############################################
murasaki-1.68.6/debian-tests-data/NZ_GG705059.gbk-7669- imbedded in a TRX fold. They function as protein disulfide
murasaki-1.68.6/debian-tests-data/NZ_GG705059.gbk:7670: isomerases and chaperones in the bacterial periplasm to
murasaki-1.68.6/debian-tests-data/NZ_GG705059.gbk-7671- correct non-native disulfide bonds...; Region:
##############################################
murasaki-1.68.6/debian/rules-33- for pscript in $(DEBMEDBIN)/* ; do \
murasaki-1.68.6/debian/rules:34: pod2man $${pscript} > $(CMANDIR)/`basename $${pscript}`.1 ; \
murasaki-1.68.6/debian/rules-35- done
##############################################
murasaki-1.68.6/debian/rules-41- for man in $(MANDIR)/*.1 ; do \
murasaki-1.68.6/debian/rules:42: cp -a $${man} $(MMANDIR)/`basename $${man} .1`-mpi.1 ; \
murasaki-1.68.6/debian/rules-43- done
##############################################
murasaki-1.68.6/.pc/spelling.patch/filter.pl-108- my $func="sub {" . join(" && ",(map {"statReqsOk('$_')"} statReqs(@_)))."}";
murasaki-1.68.6/.pc/spelling.patch/filter.pl:109: $statreqs{$_[1]}=eval($func);
murasaki-1.68.6/.pc/spelling.patch/filter.pl-110- },
##############################################
murasaki-1.68.6/.pc/spelling.patch/filter.pl-882- }
murasaki-1.68.6/.pc/spelling.patch/filter.pl:883: return eval('sub { my %stats=@_; return '.$exp.'}');
murasaki-1.68.6/.pc/spelling.patch/filter.pl-884-}
##############################################
murasaki-1.68.6/.pc/spelling.patch/filter.pl-909- print $reqs{$k}." = ";
murasaki-1.68.6/.pc/spelling.patch/filter.pl:910: $reqs{$k}=eval($reqs{$k});
murasaki-1.68.6/.pc/spelling.patch/filter.pl-911- print $reqs{$k}."\n";
##############################################
murasaki-1.68.6/.pc/spelling.patch/filter.pl-1149- print "Plotting ROC data via ROCR\n";
murasaki-1.68.6/.pc/spelling.patch/filter.pl:1150: my $RresCode=system("R --silent --vanilla --no-save < $rocrPath.R >& $rocrPath.Rout");
murasaki-1.68.6/.pc/spelling.patch/filter.pl-1151- my $Rres=slurp("$rocrPath.Rout");
##############################################
murasaki-1.68.6/.pc/spelling.patch/filter.pl-1220- my $seq=$_;
murasaki-1.68.6/.pc/spelling.patch/filter.pl:1221: my $length=`$root/geneparse.pl -lf $seq`;
murasaki-1.68.6/.pc/spelling.patch/filter.pl-1222- chomp $length;
##############################################
murasaki-1.68.6/.pc/spelling.patch/filter.pl-1241- print "CDS file not found for $seq. Generating...\n";
murasaki-1.68.6/.pc/spelling.patch/filter.pl:1242: my $res=system("$root/getcds.pl $seq");
murasaki-1.68.6/.pc/spelling.patch/filter.pl-1243- unless(-f "$seq.cds"){
##############################################
murasaki-1.68.6/.pc/spelling.patch/simpal.pl-54- die "File not found $seq" unless -e $seq;
murasaki-1.68.6/.pc/spelling.patch/simpal.pl:55: my ($fwd,$rev)=(lc `$root/geneparse -c -q $seq`,
murasaki-1.68.6/.pc/spelling.patch/simpal.pl:56: lc `$root/antisense.pl -c $seq`);
murasaki-1.68.6/.pc/spelling.patch/simpal.pl-57- my %hash;
##############################################
murasaki-1.68.6/.pc/man_syntax.patch/qlob.pl-185- print JOB "$cmd\n";
murasaki-1.68.6/.pc/man_syntax.patch/qlob.pl:186: print "Local run. Exit result: ".system($cmd)."\n" if $local;
murasaki-1.68.6/.pc/man_syntax.patch/qlob.pl-187-}
##############################################
murasaki-1.68.6/filter.pl-108- my $func="sub {" . join(" && ",(map {"statReqsOk('$_')"} statReqs(@_)))."}";
murasaki-1.68.6/filter.pl:109: $statreqs{$_[1]}=eval($func);
murasaki-1.68.6/filter.pl-110- },
##############################################
murasaki-1.68.6/filter.pl-882- }
murasaki-1.68.6/filter.pl:883: return eval('sub { my %stats=@_; return '.$exp.'}');
murasaki-1.68.6/filter.pl-884-}
##############################################
murasaki-1.68.6/filter.pl-909- print $reqs{$k}." = ";
murasaki-1.68.6/filter.pl:910: $reqs{$k}=eval($reqs{$k});
murasaki-1.68.6/filter.pl-911- print $reqs{$k}."\n";
##############################################
murasaki-1.68.6/filter.pl-1149- print "Plotting ROC data via ROCR\n";
murasaki-1.68.6/filter.pl:1150: my $RresCode=system("R --silent --vanilla --no-save < $rocrPath.R >& $rocrPath.Rout");
murasaki-1.68.6/filter.pl-1151- my $Rres=slurp("$rocrPath.Rout");
##############################################
murasaki-1.68.6/filter.pl-1220- my $seq=$_;
murasaki-1.68.6/filter.pl:1221: my $length=`$root/geneparse.pl -lf $seq`;
murasaki-1.68.6/filter.pl-1222- chomp $length;
##############################################
murasaki-1.68.6/filter.pl-1241- print "CDS file not found for $seq. Generating...\n";
murasaki-1.68.6/filter.pl:1242: my $res=system("$root/getcds.pl $seq");
murasaki-1.68.6/filter.pl-1243- unless(-f "$seq.cds"){
##############################################
murasaki-1.68.6/simpal.pl-54- die "File not found $seq" unless -e $seq;
murasaki-1.68.6/simpal.pl:55: my ($fwd,$rev)=(lc `$root/geneparse -c -q $seq`,
murasaki-1.68.6/simpal.pl:56: lc `$root/antisense.pl -c $seq`);
murasaki-1.68.6/simpal.pl-57- my %hash;
##############################################
murasaki-1.68.6/qlob.pl-185- print JOB "$cmd\n";
murasaki-1.68.6/qlob.pl:186: print "Local run. Exit result: ".system($cmd)."\n" if $local;
murasaki-1.68.6/qlob.pl-187-}