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/dports/biology/infernal/infernal-1.1.3/hmmer/profmark/
H A Dx-phmmer-consensus17 $resultdir = shift;
40 $output = `$hmmbuild $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
41 if ($? != 0) { die "FAILED: $hmmbuild $resultdir/$msaname.hmm $resultdir/$msaname.sto"; }
43 $output = `$hmmemit -o $resultdir/$msaname.query.fa $resultdir/$msaname.hmm`;
44 if ($? != 0) { die "FAILED: hmmemit -o $resultdir/$msaname.query.fa $resultdir/$msaname.hmm"; }
48 …if ($? != 0) { die "FAILED: $phmmer --tblout $resultdir/$msaname.tmp $opts $resultdir/$msaname.que…
50 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
58 unlink "$resultdir/$msaname.tmp";
59 unlink "$resultdir/$msaname.query.fa";
60 unlink "$resultdir/$msaname.hmm";
[all …]
H A Dx-hmmsearch17 $resultdir = shift;
33 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
41 $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
44 $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
45 …if ($? != 0) { die "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto";…
47 …$status = system("$hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm …
48 …tatus != 0) { die "FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msa…
50 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
61 unlink "$resultdir/$msaname.hmm";
62 unlink "$resultdir/$msaname.sto";
[all …]
H A Dx-hmmsearch-max17 $resultdir = shift;
33 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
41 $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
44 $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
45 …if ($? != 0) { die "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto";…
47 …$status = system("$hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm …
48 …tatus != 0) { die "FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msa…
50 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
61 unlink "$resultdir/$msaname.hmm";
62 unlink "$resultdir/$msaname.sto";
[all …]
H A Dx-h2-fs17 $resultdir = shift;
38 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
47 $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
48 if ($?) { print "FAILED: esl-afetch -o $resultdir/$msaname.sto $msafile $msaname\n"; next MSA; }
50 $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
51 …if ($?) { print "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto\n"; …
53 $output = `$hmmcalibrate $calibrateopts $resultdir/$msaname.hmm`;
56 if (! open(HMMSEARCH, "$hmmsearch $searchopts $resultdir/$msaname.hmm $fafile 2> /dev/null |"))
57 { print "FAILED: $hmmsearch $searchopts $resultdir/$msaname.hmm $fafile\n"; next MSA; }
72 unlink "$resultdir/$msaname.hmm";
[all …]
H A Dx-h2-ls17 $resultdir = shift;
38 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
47 $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
48 if ($?) { print "FAILED: esl-afetch -o $resultdir/$msaname.sto $msafile $msaname\n"; next MSA; }
50 $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
51 …if ($?) { print "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto\n"; …
53 $output = `$hmmcalibrate $calibrateopts $resultdir/$msaname.hmm`;
56 if (! open(HMMSEARCH, "$hmmsearch $searchopts $resultdir/$msaname.hmm $fafile 2> /dev/null |"))
57 { print "FAILED: $hmmsearch $searchopts $resultdir/$msaname.hmm $fafile\n"; next MSA; }
72 unlink "$resultdir/$msaname.hmm";
[all …]
H A Dpmark-master.pl50 $resultdir = shift;
59 if (-e $resultdir) { die("$resultdir exists");}
60 system("mkdir $resultdir");
89 open(SUBTBL, ">$resultdir/tbl.$i") || die ("Failed to create $resultdir/tbl.$i");
96 open(SLURMSCRIPT, ">$resultdir.sh") || die("failed to create slurm script");
104 #SBATCH -o $resultdir/tbl.%a.slurm
105 …ark_script $top_builddir $top_srcdir $resultdir $resultdir/tbl.\${SLURM_ARRAY_TASK_ID} $msafile $f…
111 system("sbatch --array=0-$maxi $resultdir.sh");
/dports/biology/hmmer/hmmer-3.3/profmark/
H A Dx-phmmer-consensus17 $resultdir = shift;
40 $output = `$hmmbuild $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
41 if ($? != 0) { die "FAILED: $hmmbuild $resultdir/$msaname.hmm $resultdir/$msaname.sto"; }
43 $output = `$hmmemit -o $resultdir/$msaname.query.fa $resultdir/$msaname.hmm`;
44 if ($? != 0) { die "FAILED: hmmemit -o $resultdir/$msaname.query.fa $resultdir/$msaname.hmm"; }
48 …if ($? != 0) { die "FAILED: $phmmer --tblout $resultdir/$msaname.tmp $opts $resultdir/$msaname.que…
50 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
58 unlink "$resultdir/$msaname.tmp";
59 unlink "$resultdir/$msaname.query.fa";
60 unlink "$resultdir/$msaname.hmm";
[all …]
H A Dx-hmmsearch17 $resultdir = shift;
33 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
41 $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
44 $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
45 …if ($? != 0) { die "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto";…
47 …$status = system("$hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm …
48 …tatus != 0) { die "FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msa…
50 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
61 unlink "$resultdir/$msaname.hmm";
62 unlink "$resultdir/$msaname.sto";
[all …]
H A Dx-hmmsearch-max17 $resultdir = shift;
33 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
41 $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
44 $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
45 …if ($? != 0) { die "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto";…
47 …$status = system("$hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm …
48 …tatus != 0) { die "FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msa…
50 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
61 unlink "$resultdir/$msaname.hmm";
62 unlink "$resultdir/$msaname.sto";
[all …]
H A Dx-h2-fs17 $resultdir = shift;
38 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
47 $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
48 if ($?) { print "FAILED: esl-afetch -o $resultdir/$msaname.sto $msafile $msaname\n"; next MSA; }
50 $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
51 …if ($?) { print "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto\n"; …
53 $output = `$hmmcalibrate $calibrateopts $resultdir/$msaname.hmm`;
56 if (! open(HMMSEARCH, "$hmmsearch $searchopts $resultdir/$msaname.hmm $fafile 2> /dev/null |"))
57 { print "FAILED: $hmmsearch $searchopts $resultdir/$msaname.hmm $fafile\n"; next MSA; }
72 unlink "$resultdir/$msaname.hmm";
[all …]
H A Dx-h2-ls17 $resultdir = shift;
38 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
47 $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
48 if ($?) { print "FAILED: esl-afetch -o $resultdir/$msaname.sto $msafile $msaname\n"; next MSA; }
50 $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
51 …if ($?) { print "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto\n"; …
53 $output = `$hmmcalibrate $calibrateopts $resultdir/$msaname.hmm`;
56 if (! open(HMMSEARCH, "$hmmsearch $searchopts $resultdir/$msaname.hmm $fafile 2> /dev/null |"))
57 { print "FAILED: $hmmsearch $searchopts $resultdir/$msaname.hmm $fafile\n"; next MSA; }
72 unlink "$resultdir/$msaname.hmm";
[all …]
H A Dpmark-master.pl50 $resultdir = shift;
59 if (-e $resultdir) { die("$resultdir exists");}
60 system("mkdir $resultdir");
89 open(SUBTBL, ">$resultdir/tbl.$i") || die ("Failed to create $resultdir/tbl.$i");
96 open(SLURMSCRIPT, ">$resultdir.sh") || die("failed to create slurm script");
104 #SBATCH -o $resultdir/tbl.%a.slurm
105 …ark_script $top_builddir $top_srcdir $resultdir $resultdir/tbl.\${SLURM_ARRAY_TASK_ID} $msafile $f…
111 system("sbatch --array=0-$maxi $resultdir.sh");
/dports/biology/infernal/infernal-1.1.3/rmark/
H A Dx-cmsearch99 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
158 …$status = system("$cmbuild $buildopts $resultdir/$msaname" . $key . ".cm $resultdir/$msaname" . $k…
160 $cmfile = "$resultdir/$msaname" . $key . ".cm";
165 $cmfile = "$resultdir/$msaname" . $key . ".cm";
179 …$command = "$sfetch -o $resultdir/$msaname" . $key . ".pfa -f $orig_fafile $resultdir/$msaname" . …
183 $fafile = "$resultdir/$msaname" . $key . ".pfa";
196 …$command = "$sfetch -o $resultdir/$msaname" . $key . ".wpfa -f $orig_fafile $resultdir/$msaname" .…
200 $fafile = "$resultdir/$msaname" . $key . ".wpfa";
252 unlink "$resultdir/$msaname" . $key . ".tmp";
270 …system("grep \"CPU time\" $resultdir/$msaname" . $key . ".search > $resultdir/$msaname" . $key . "…
[all …]
H A Drmark-master.pl165 if ($do_force && (-e $resultdir)) {
166 system("rm -rf $resultdir");
168 if(-e $resultdir) {
169 die("$resultdir exists");
171 system("mkdir $resultdir");
174 if(! -e $resultdir) {
226 open(SUBTBL, ">$resultdir/tbl.$i") || die ("Failed to create $resultdir/tbl.$i");
268 …resultdir.$i -j y -o $resultdir/tbl$i.sge -R y -l excl=true '$rmark_script $posonly_opt $poswindow…
272 …resultdir.$i -j y -o $resultdir/tbl$i.sge -R y -l excl=true '$rmark_script $posonly_opt $poswindow…
293 …resultdir.$i.$j.T -j y -o $resultdir/tbl$i.$j.T.sge -R y -l excl=true '$rmark_script -K $j.T -T $p…
[all …]
H A Dx-nhmmer57 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
102 …$command = "$sfetch -o $resultdir/$msaname.pfa -f $orig_fafile $resultdir/$msaname.sfetch > /dev/n…
106 $fafile = "$resultdir/$msaname.pfa";
109 …us = system("$nhmmer $searchopts --tblout $resultdir/$msaname.tmp $modeldir/$msaname.hmm $fafile >…
110 …die "FAILED: $nhmmer $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile …
112 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
128 unlink "$resultdir/$msaname.tmp";
129 unlink "$resultdir/$msaname.search";
132 unlink "$resultdir/$msaname.pfa";
133 unlink "$resultdir/$msaname.sfetch";
[all …]
H A Dx-nhmmer2cmsearch60 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
153 …opts $fam_searchopts_H{$msaname} --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile …
157 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
194 $filtered_db = "$resultdir/$msaname.sub.fa";
215 …open(OUTPUT, "$resultdir/$msaname.tmp") || die "FAILED: to open $resultdir/$msaname.tmp tabular ou…
247 unlink "$resultdir/$msaname.tmp";
251 system("grep \"CPU time\" $resultdir/$msaname.search1 > $resultdir/$msaname.time");
252 system("grep \"CPU time\" $resultdir/$msaname.search >> $resultdir/$msaname.time");
254 unlink "$resultdir/$msaname.search";
257 unlink "$resultdir/$msaname.cm";
[all …]
/dports/biology/infernal/infernal-1.1.3/hmmer/test-speed/
H A Dx-sam14 $resultdir = shift;
28 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
44 $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
48 $output = `esl-reformat -o $resultdir/$msaname.a2m a2m $resultdir/$msaname.sto`;
52 `(cd $resultdir; $w05 $msaname.a2m $msaname.mod &> /dev/null)`;
62 $output = `(cd $resultdir; $hmmscore $msaname -i $msaname.mod -db ../$targetdb -sw 2 2>&1)`;
71 open (SAMOUTPUT,"$resultdir/$msaname.dist") || die "FAILED: opening sam output on $msaname\n";
88 unlink "$resultdir/$msaname.sto";
89 unlink "$resultdir/$msaname.a2m";
90 unlink "$resultdir/$msaname.mod";
[all …]
H A Dspeed-master.pl52 $resultdir = shift;
61 if (-e $resultdir) { die("$resultdir exists");}
62 system("mkdir $resultdir");
79 open(SUBTBL, ">$resultdir/tbl.$i") || die ("Failed to create $resultdir/tbl.$i");
91 open(SLURMSCRIPT, ">$resultdir.sh") || die("failed to create slurm script");
99 #SBATCH -o $resultdir/tbl.%a.slurm
100 …river $top_builddir $top_srcdir $resultdir $resultdir/tbl.\${SLURM_ARRAY_TASK_ID} $nthread $queryd…
106 system("sbatch --array=0-$maxidx $resultdir.sh");
H A Dx-psiblast15 $resultdir = shift;
28 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
43 $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
47 $output = `esl-reformat -o $resultdir/$msaname.pbl psiblast $resultdir/$msaname.sto`;
51 $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
56 $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
61 …$output = `$blastpgp $blastopts -d $targetdb -i $resultdir/$msaname.query.fa -B $resultdir/$msanam…
66 …$output = `$blastpgp $blastopts -d $targetdb -i $resultdir/$msaname.query.fa -B $resultdir/$msanam…
H A Dx-fasta15 $resultdir = shift;
29 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
44 $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
48 $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
53 $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
57 if ($n == 1) { $output = `$fasta $fasta_opts $resultdir/$msaname.query.fa $targetdb 2>&1`; }
61 $output = `$fasta $fasta_opts $resultdir/$msaname.query.fa $targetdb 2>&1`;
75 unlink "$resultdir/$msaname.sto";
76 unlink "$resultdir/$msaname.query.fa";
H A Dx-hmmer215 $resultdir = shift;
30 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
49 $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
53 $output = `$hmmbuild -F --amino $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
56 $output = `grep "^LENG" $resultdir/$msaname.hmm`;
61 if ($n == 1) { $output = `$hmmsearch $opts $resultdir/$msaname.hmm $targetdb 2>&1`; }
64 $output = `$hmmsearch $opts $resultdir/$msaname.hmm $targetdb 2>&1`;
75 unlink "$resultdir/$msaname.sto";
76 unlink "$resultdir/$msaname.hmm";
H A Dx-ncbiblast+15 $resultdir = shift;
28 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
43 $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
47 $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
52 $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
56 if ($n==1) { `$blastp $blastopts -db $targetdb -query $resultdir/$msaname.query.fa 2>&1`; }
60 $output = `$blastp $blastopts -db $targetdb -query $resultdir/$msaname.query.fa 2>&1`;
74 unlink "$resultdir/$msaname.sto";
75 unlink "$resultdir/$msaname.query.fa";
/dports/biology/hmmer/hmmer-3.3/test-speed/
H A Dx-sam14 $resultdir = shift;
28 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
44 $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
48 $output = `esl-reformat -o $resultdir/$msaname.a2m a2m $resultdir/$msaname.sto`;
52 `(cd $resultdir; $w05 $msaname.a2m $msaname.mod &> /dev/null)`;
62 $output = `(cd $resultdir; $hmmscore $msaname -i $msaname.mod -db ../$targetdb -sw 2 2>&1)`;
71 open (SAMOUTPUT,"$resultdir/$msaname.dist") || die "FAILED: opening sam output on $msaname\n";
88 unlink "$resultdir/$msaname.sto";
89 unlink "$resultdir/$msaname.a2m";
90 unlink "$resultdir/$msaname.mod";
[all …]
H A Dspeed-master.pl52 $resultdir = shift;
61 if (-e $resultdir) { die("$resultdir exists");}
62 system("mkdir $resultdir");
79 open(SUBTBL, ">$resultdir/tbl.$i") || die ("Failed to create $resultdir/tbl.$i");
91 open(SLURMSCRIPT, ">$resultdir.sh") || die("failed to create slurm script");
99 #SBATCH -o $resultdir/tbl.%a.slurm
100 …river $top_builddir $top_srcdir $resultdir $resultdir/tbl.\${SLURM_ARRAY_TASK_ID} $nthread $queryd…
106 system("sbatch --array=0-$maxidx $resultdir.sh");
H A Dx-psiblast15 $resultdir = shift;
28 if (! -e $resultdir) { die "$resultdir doesn't exist"; }
43 $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
47 $output = `esl-reformat -o $resultdir/$msaname.pbl psiblast $resultdir/$msaname.sto`;
51 $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
56 $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
61 …$output = `$blastpgp $blastopts -d $targetdb -i $resultdir/$msaname.query.fa -B $resultdir/$msanam…
66 …$output = `$blastpgp $blastopts -d $targetdb -i $resultdir/$msaname.query.fa -B $resultdir/$msanam…

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