===========================================================
                                      .___ __  __   
          _________________  __ __  __| _/|__|/  |_ 
         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
prokka-1.14.6+dfsg/.travis.yml-19-    - "prokka --listdb"
prokka-1.14.6+dfsg/.travis.yml:20:    - "prokka --cpus 2 --outdir asm --prefix asm test/plasmid.fna"
prokka-1.14.6+dfsg/.travis.yml-21-    - "grep '>' asm/asm.fna"
##############################################
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-58-print STDERR "Untarring $lib files from: $tarfile\n";
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm:59:system("tar -C $tempdir -f $tarfile -z -x --wildcards '$lib*'");
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-60-
##############################################
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-65-  my $faln = "$tempdir/$cid.FASTA";
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm:66:#  system("esl-reformat stockholm $tempdir/$cid.FASTA | grep -v lcl.consensus > $faln");
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-67-  print STDERR "$cid | $faln >> $lib.aln\n";
##############################################
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-88-  }
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm:89:#  system("cat $faln $lib.aln");
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-90-#  exit(-1);
##############################################
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-92-
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm:93:system("hmmbuild $lib.hmm.ascii $lib.aln");
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-94-
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-95-print STDERR "Created $lib.hmm.ascii file - converting to $lib.hmm binary format.\n";
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm:96:system("hmmconvert -b $lib.hmm.ascii > $lib.hmm");
prokka-1.14.6+dfsg/bin/prokka-cdd_to_hmm-97-
##############################################
prokka-1.14.6+dfsg/bin/prokka-clusters_to_hmm-48-print STDERR "Extracting alignments: $cmd\n";
prokka-1.14.6+dfsg/bin/prokka-clusters_to_hmm:49:system($cmd);
prokka-1.14.6+dfsg/bin/prokka-clusters_to_hmm-50-my @msa = <$tmp/*.aln>;
##############################################
prokka-1.14.6+dfsg/bin/prokka-clusters_to_hmm-70-print STDERR "\nPressing indices: $out_fn\n";
prokka-1.14.6+dfsg/bin/prokka-clusters_to_hmm:71:system("hmmpress $out_fn");
prokka-1.14.6+dfsg/bin/prokka-clusters_to_hmm-72-
##############################################
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm-58-  print STDERR "Extracting $aln_file.\n";
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm:59:  system("tar -C $dir --strip-components 1 -zxf $aln_file")==0 or die "ERROR: $?";
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm-60-  my @msa = <$dir/*.msa>;
##############################################
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm-68-      $desc =~ s{'}{\\'}g;
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm:69:      system( "hmmbuild -o /dev/null -n $id /dev/stdout $msa | sed \"3i DESC  $desc\" > $dir/$id.hmm" )==0 or die "ERROR: $?";
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm-70-#      if ($id eq 'MF_00023') {
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm:71:#        system("head -20 $dir/$id.hmm");
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm-72-#        last;
##############################################
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm-86-print STDERR "Combining into $dest\n";
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm:87:system("cat $dir/*.hmm > $dest");
prokka-1.14.6+dfsg/bin/prokka-hamap_to_hmm-88-
##############################################
prokka-1.14.6+dfsg/debian/createmanpages-4-
prokka-1.14.6+dfsg/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
prokka-1.14.6+dfsg/debian/createmanpages-6-
##############################################
prokka-1.14.6+dfsg/debian/rules-16-override_dh_link:
prokka-1.14.6+dfsg/debian/rules:17:	for db in `find debian/$(DEB_SOURCE)/usr/share/prokka/db -type f` ; do \
prokka-1.14.6+dfsg/debian/rules:18:	    vardir=`echo $${db} | sed -e 's?.*/usr/share?/var/lib?'` ; \
prokka-1.14.6+dfsg/debian/rules:19:	    mkdir -p debian/$(DEB_SOURCE)/`dirname $${vardir}` ; \
prokka-1.14.6+dfsg/debian/rules:20:	    usrdir=`echo $${db} | sed -e 's?.*/usr?/usr?'` ; \
prokka-1.14.6+dfsg/debian/rules-21-	    dh_link $${usrdir} $${vardir} ; \
##############################################
prokka-1.14.6+dfsg/debian/tests/sample-programs-9-prokka --listdb
prokka-1.14.6+dfsg/debian/tests/sample-programs:10:prokka --cpus $(nproc) --outdir "${AUTOPKGTEST_TMP}"/asm --prefix asm test/plasmid.fna
prokka-1.14.6+dfsg/debian/tests/sample-programs-11-grep '>' "${AUTOPKGTEST_TMP}"/asm/asm.fna