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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
hhsuite-3.3.0+ds/data/query.hhr-2305- +-|-|||. |.+-|.+..||--|..-.|.-..--...-.-+|.|.+.|-.|+-.-|----||--|.--|
hhsuite-3.3.0+ds/data/query.hhr:2306:T Consensus 227 llypgdll------heaghlavmpperrnaekpsssdpaeemasiawswaaaihlgipaevvfhehgyrgqasm 294 (364)
hhsuite-3.3.0+ds/data/query.hhr:2307:T UP20|MIBBOBABA 227 LLYPGDLL------HEAGHLAVMPPERRNAEKPSSSDPAEEMASIAWSWAAAIHLGIPAEVVFHEHGYRGQASM 294 (364)
hhsuite-3.3.0+ds/data/query.hhr-2308-Confidence 44777764 788899999998887776666666666777899999999888764332222444444333
##############################################
hhsuite-3.3.0+ds/lib/ffindex/src/ext/CMakeLists.txt:1:include(${CMAKE_ROOT}/Modules/CheckFunctionExists.cmake)
hhsuite-3.3.0+ds/lib/ffindex/src/ext/CMakeLists.txt-2-check_function_exists(fmemopen HAVE_FMEMOPEN)
##############################################
hhsuite-3.3.0+ds/scripts/HHPaths.pm-78- if ($v>=2) {printf(STDERR "\$ %s\n",$_[0]);}
hhsuite-3.3.0+ds/scripts/HHPaths.pm:79: system($_[0]);
hhsuite-3.3.0+ds/scripts/HHPaths.pm-80- if ($? == -1) {
##############################################
hhsuite-3.3.0+ds/scripts/mergeali.pl-179- if (-e $alifilefas) {
hhsuite-3.3.0+ds/scripts/mergeali.pl:180: &HHPaths::System("perl $hhscripts/reformat.pl -M first $alifilefas $alifile");
hhsuite-3.3.0+ds/scripts/mergeali.pl-181- last;
##############################################
hhsuite-3.3.0+ds/scripts/mergeali.pl-186- if ($diff ne "") {
hhsuite-3.3.0+ds/scripts/mergeali.pl:187: &HHPaths::System("hhfilter -v $v -i $alifile -o $tmpfile -diff $diff -cov 5");
hhsuite-3.3.0+ds/scripts/mergeali.pl-188- $alifile=$tmpfile;
##############################################
hhsuite-3.3.0+ds/scripts/mergeali.pl-261- if (-e $alifilefas) {
hhsuite-3.3.0+ds/scripts/mergeali.pl:262: &HHPaths::System("perl $hhscripts/reformat.pl -M first $alifilefas $alifile");
hhsuite-3.3.0+ds/scripts/mergeali.pl-263- last;
##############################################
hhsuite-3.3.0+ds/scripts/mergeali.pl-268- if ($diff ne "") {
hhsuite-3.3.0+ds/scripts/mergeali.pl:269: &HHPaths::System("hhfilter -v $v -i $alifile -o $tmpfile -diff $diff -cov 5");
hhsuite-3.3.0+ds/scripts/mergeali.pl-270- $alifile=$tmpfile;
##############################################
hhsuite-3.3.0+ds/scripts/mergeali.pl-489-}
hhsuite-3.3.0+ds/scripts/mergeali.pl:490:#&HHPaths::System("perl $hhscripts/reformat.pl $baseout.a3m $baseout.fas -v 3");
hhsuite-3.3.0+ds/scripts/mergeali.pl-491-# Reformat $baseout.a3m such that match columns are defined by first seed sequence?
hhsuite-3.3.0+ds/scripts/mergeali.pl:492:#&HHPaths::System("perl $hhscripts/reformat.pl -M first $baseout.fas $baseout"."_first.a3m");
hhsuite-3.3.0+ds/scripts/mergeali.pl-493-
##############################################
hhsuite-3.3.0+ds/scripts/multithread.pl-134- $lcommand=~s/\$base/$base/g;
hhsuite-3.3.0+ds/scripts/multithread.pl:135: &System("$lcommand");
hhsuite-3.3.0+ds/scripts/multithread.pl-136- if ($v>=2) {printf("\nProcess $$ for file %s (%i) finished.",$file,$ifile);}
##############################################
hhsuite-3.3.0+ds/scripts/multithread.pl-173- if ($v>=1) {print("\n".$_[0]," ");}
hhsuite-3.3.0+ds/scripts/multithread.pl:174: if (system($_[0])) {
hhsuite-3.3.0+ds/scripts/multithread.pl-175-# Why is always -1 returned???
##############################################
hhsuite-3.3.0+ds/scripts/pdb2fasta.pl-93- my @sequences=(); # contains all sequences of chains to be printed to outfile
hhsuite-3.3.0+ds/scripts/pdb2fasta.pl:94: my @resolution=(); # $resolution[$nc] contains resolution of $nc'th sequence, where $nc=$nchains{$seqres}
hhsuite-3.3.0+ds/scripts/pdb2fasta.pl-95- my %nchains; # $nchains{$seqres} is index in @sequences of sequence with these residues
##############################################
hhsuite-3.3.0+ds/scripts/pdbfilter.pl-145-&PrintSequences("$root.db",$nold);
hhsuite-3.3.0+ds/scripts/pdbfilter.pl:146:&System("$ncbidir/formatdb -i $root.db");
hhsuite-3.3.0+ds/scripts/pdbfilter.pl-147-my $nacc=0; # number of accepted sequences = number of BLAST searches already performed
##############################################
hhsuite-3.3.0+ds/scripts/pdbfilter.pl-174- &PrintSequences("$root.db",$done);
hhsuite-3.3.0+ds/scripts/pdbfilter.pl:175: &System("$ncbidir/formatdb -i $root.db");
hhsuite-3.3.0+ds/scripts/pdbfilter.pl-176- $reformat+=$step;
##############################################
hhsuite-3.3.0+ds/scripts/pdbfilter.pl-349- $v--;
hhsuite-3.3.0+ds/scripts/pdbfilter.pl:350: &HHPaths::System($_[0]);
hhsuite-3.3.0+ds/scripts/pdbfilter.pl-351- $v++;
##############################################
hhsuite-3.3.0+ds/scripts/addss.pl-183- else {
hhsuite-3.3.0+ds/scripts/addss.pl:184: &HHPaths::System("cp $infile $tmpfile.1.in.a3m");
hhsuite-3.3.0+ds/scripts/addss.pl-185- }
##############################################
hhsuite-3.3.0+ds/scripts/addss.pl-515-
hhsuite-3.3.0+ds/scripts/addss.pl:516: &HHPaths::System("rm $tmpfile.mtx $tmpfile.ss $tmpfile.ss2");
hhsuite-3.3.0+ds/scripts/addss.pl-517- if ( $v >= 2 ) {
##############################################
hhsuite-3.3.0+ds/scripts/addss.pl-557-
hhsuite-3.3.0+ds/scripts/addss.pl:558: &HHPaths::System("cp $infile $dummydb");
hhsuite-3.3.0+ds/scripts/addss.pl:559: &HHPaths::System("$ncbidir/formatdb -i $dummydb");
hhsuite-3.3.0+ds/scripts/addss.pl-560- if ( !-e "$dummydb.phr" ) {
##############################################
hhsuite-3.3.0+ds/scripts/addss.pl-570- #print("Predicting secondary structure...\n");
hhsuite-3.3.0+ds/scripts/addss.pl:571: &HHPaths::System( "echo " . "$tmpfile_no_dir" . ".chk > $tmpfile.pn\n" );
hhsuite-3.3.0+ds/scripts/addss.pl:572: &HHPaths::System( "echo " . "$tmpfile_no_dir" . ".sq > $tmpfile.sn\n" );
hhsuite-3.3.0+ds/scripts/addss.pl:573: &HHPaths::System("$ncbidir/makemat -P $tmpfile");
hhsuite-3.3.0+ds/scripts/addss.pl-574-
##############################################
hhsuite-3.3.0+ds/scripts/addss.pl-718- # Thanks to Stefan Bienert for this patch
hhsuite-3.3.0+ds/scripts/addss.pl:719: &HHPaths::System("$dssp -i $pdbfile -o $dsspfile 2> /dev/null");
hhsuite-3.3.0+ds/scripts/addss.pl-720-
##############################################
hhsuite-3.3.0+ds/scripts/addss.pl-945- (undef, $tmp_pdb_filename) = tempfile(UNLINK => 1, OPEN => 0);
hhsuite-3.3.0+ds/scripts/addss.pl:946: &HHPaths::System("gunzip -c $pdbfile > $tmp_pdb_filename");
hhsuite-3.3.0+ds/scripts/addss.pl-947- return "$tmp_pdb_filename";
##############################################
hhsuite-3.3.0+ds/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
hhsuite-3.3.0+ds/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
hhsuite-3.3.0+ds/debian/tests/run-unit-test-8- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/multithread.pl-134- $lcommand=~s/\$base/$base/g;
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/multithread.pl:135: &System("$lcommand");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/multithread.pl-136- if ($v>=2) {printf("\nProcess $$ for file %s (%i) finished.",$file,$ifile);}
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/multithread.pl-173- if ($v>=1) {print("\n".$_[0]," ");}
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/multithread.pl:174: if (system($_[0])) {
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/multithread.pl-175-# Why is always -1 returned???
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdb2fasta.pl-93- my @sequences=(); # contains all sequences of chains to be printed to outfile
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdb2fasta.pl:94: my @resolution=(); # $resolution[$nc] contains resolution of $nc'th sequence, where $nc=$nchains{$seqres}
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdb2fasta.pl-95- my %nchains; # $nchains{$seqres} is index in @sequences of sequence with these residues
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl-145-&PrintSequences("$root.db",$nold);
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl:146:&System("$ncbidir/formatdb -i $root.db");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl-147-my $nacc=0; # number of accepted sequences = number of BLAST searches already performed
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl-174- &PrintSequences("$root.db",$done);
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl:175: &System("$ncbidir/formatdb -i $root.db");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl-176- $reformat+=$step;
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl-349- $v--;
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl:350: &HHPaths::System($_[0]);
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/pdbfilter.pl-351- $v++;
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-183- else {
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:184: &HHPaths::System("cp $infile $tmpfile.1.in.a3m");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-185- }
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-515-
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:516: &HHPaths::System("rm $tmpfile.mtx $tmpfile.ss $tmpfile.ss2");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-517- if ( $v >= 2 ) {
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-557-
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:558: &HHPaths::System("cp $infile $dummydb");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:559: &HHPaths::System("$ncbidir/formatdb -i $dummydb");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-560- if ( !-e "$dummydb.phr" ) {
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-570- #print("Predicting secondary structure...\n");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:571: &HHPaths::System( "echo " . "$tmpfile_no_dir" . ".chk > $tmpfile.pn\n" );
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:572: &HHPaths::System( "echo " . "$tmpfile_no_dir" . ".sq > $tmpfile.sn\n" );
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:573: &HHPaths::System("$ncbidir/makemat -P $tmpfile");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-574-
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-718- # Thanks to Stefan Bienert for this patch
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:719: &HHPaths::System("$dssp -i $pdbfile -o $dsspfile 2> /dev/null");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-720-
##############################################
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-945- (undef, $tmp_pdb_filename) = tempfile(UNLINK => 1, OPEN => 0);
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl:946: &HHPaths::System("gunzip -c $pdbfile > $tmp_pdb_filename");
hhsuite-3.3.0+ds/.pc/perlscript_uselib/scripts/addss.pl-947- return "$tmp_pdb_filename";