=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ 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