$fafile (reference) in projects: dports

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Searched refs:fafile (Results 1 – 25 of 62) sorted by relevance

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/dports/biology/infernal/infernal-1.1.3/hmmer/testsuite/
H A D	i4-zerolength-seqs.sh	`33 fafile=$tmppfx.fa 35 cat > $fafile <<EOF 41 $hmmscan $hmmfile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi 42 $hmmsearch $hmmfile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi 43 $phmmer $fafile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi 44 $jackhmmer $fafile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi 48 rm $fafile`
H A D	i13-msa-integrity.pl	59 my ($fafile, $hmmfile) = @_; 61 `$builddir/src/hmmalign -o $tmppfx.sto $hmmfile $fafile > /dev/null 2>&1`; 67 `$builddir/easel/miniapps/esl-reformat -u fasta $fafile > $tmppfx.fa2 2>/dev/null`; 78 my ($fafile, $hmmfile) = @_; 82 …search -E 0.01 --domE 0.01 -A $tmppfx.sto --domtbl $tmppfx.dtbl $hmmfile $fafile > /dev/null 2>&1`; 88 `$builddir/easel/miniapps/esl-sfetch --index $fafile > /dev/null 2>&1`; 94 `$builddir/easel/miniapps/esl-sfetch -Cf $fafile $tmppfx.gdf > $tmppfx.fa3`;
/dports/biology/hmmer/hmmer-3.3/testsuite/
H A D	i4-zerolength-seqs.sh	`33 fafile=$tmppfx.fa 35 cat > $fafile <<EOF 41 $hmmscan $hmmfile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi 42 $hmmsearch $hmmfile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi 43 $phmmer $fafile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi 44 $jackhmmer $fafile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi 48 rm $fafile`
H A D	i13-msa-integrity.pl	59 my ($fafile, $hmmfile) = @_; 61 `$builddir/src/hmmalign -o $tmppfx.sto $hmmfile $fafile > /dev/null 2>&1`; 67 `$builddir/easel/miniapps/esl-reformat -u fasta $fafile > $tmppfx.fa2 2>/dev/null`; 78 my ($fafile, $hmmfile) = @_; 82 …search -E 0.01 --domE 0.01 -A $tmppfx.sto --domtbl $tmppfx.dtbl $hmmfile $fafile > /dev/null 2>&1`; 88 `$builddir/easel/miniapps/esl-sfetch --index $fafile > /dev/null 2>&1`; 94 `$builddir/easel/miniapps/esl-sfetch -Cf $fafile $tmppfx.gdf > $tmppfx.fa3`;
/dports/biology/infernal/infernal-1.1.3/testsuite/
H A D	itest3-msa-integrity.pl	58 my ($fafile, $cmfile) = @_; 60 `$builddir/src/cmalign -o $tmppfx.sto $cmfile $fafile > /dev/null 2>&1`; 66 `$builddir/easel/miniapps/esl-reformat -r -u fasta $fafile > $tmppfx.fa2 2>/dev/null`; 77 my ($fafile, $cmfile) = @_; 81 …`$builddir/src/cmsearch -E 1 --incE 1 --tblout $tmppfx.tbl -A $tmppfx.sto $cmfile $fafile > /dev/n… 87 `$builddir/easel/miniapps/esl-sfetch --index $fafile > /dev/null 2>&1`; 93 `$builddir/easel/miniapps/esl-sfetch -Cf $fafile $tmppfx.gdf > $tmppfx.fa3`;
/dports/biology/infernal/infernal-1.1.3/rmark/
H A D	x-nhmmer2cmsearch	42 ($execdir, $scriptdir, $modeldir, $resultdir, $optsfile, $tblfile, $msafile, $posfile, $fafile, $ou… 99 if(! -e "$fafile.ssi") { 100 $status = system("$sfetch --index $fafile"); 101 if ($status != 0) { die "FAILED: $sfetch --index $fafile"; } 107 $output = `$seqstat -a $fafile`; 152 …pts_H{$msaname} --tblout $resultdir/$msaname.tmp $modeldir/$msaname.hmm $fafile > $resultdir/$msan… 195 if(! -e "$fafile.ssi") { 196 $status = system("$sfetch --index $fafile"); 197 if ($status != 0) { die "FAILED: $sfetch --index $fafile"; } 199 $status = system("$sfetch -Cf $fafile $sfetch_in > $filtered_db"); [all …]
H A D	rmark-master.pl	118 $fafile = "$benchmark_pfx.fa"; 152 if (! -e $fafile) { die "$fafile doesn't exist"; } 157 $fafile = $pfafile; 161 $fafile = $wpfafile; 179 $fafile = $npfafile; 268 …tdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.o… 272 …tdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.o… 281 $fafile = $fafileA[$j]; 286 …ptdir $modeldir $resultdir $optsfile $resultdir/tbl$i $msafile $posfile $fafile $resultdir/tbl$i.$… 293 …tdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.$… [all …]
H A D	x-nhmmer	`34 ($execdir, $scriptdir, $modeldir, $resultdir, $optsfile, $tblfile, $msafile, $posfile, $fafile, $ou… 85 $orig_fafile = $fafile; 106 $fafile = "$resultdir/$msaname.pfa"; 109 …mer $searchopts --tblout $resultdir/$msaname.tmp $modeldir/$msaname.hmm $fafile > $resultdir/$msan… 110 …er $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > $resultdir/$msan…`
H A D	x-rfamscan	50 ($execdir, $scriptdir, $modeldir, $resultdir, $optsfile, $tblfile, $msafile, $posfile, $fafile, $ou… 120 if(! -e "$fafile.ssi") { 121 $status = system("$sfetch --index $fafile"); 122 if ($status != 0) { die "FAILED: $sfetch --index $fafile"; } 128 $output = `$seqstat -a $fafile`; 146 $orig_fafile = $fafile; 180 …$command = "$wublastn $fafile $resultdir/$msaname.query mformat=3 cpus=1 $specsearchopts $fam_sear… 185 …$command = "$wublastn $fafile $resultdir/$msaname.query mformat=3 cpus=1 $senssearchopts $fam_sear… 223 $status = system("$sfetch -Cf $fafile $sfetch_in > $filtered_db"); 224 if ($status != 0) { die "FAILED: $sfetch -Cf $fafile $sfetch_in > $filtered_db"; }
H A D	x-cmsearch	`66 ($execdir, $scriptdir, $modeldir, $resultdir, $optsfile, $tblfile, $msafile, $posfile, $fafile, $ou… 149 $orig_fafile = $fafile; 183 $fafile = "$resultdir/$msaname" . $key . ".pfa"; 200 $fafile = "$resultdir/$msaname" . $key . ".wpfa"; 212 …pts $fam_searchopts_H{$msaname} $p7file_opt $tab_opt $extra_opt $cmfile $fafile > $resultdir/$msan… 217 …pts $fam_searchopts_H{$msaname} $p7file_opt $tab_opt $extra_opt $cmfile $fafile > $resultdir/$msan…`
/dports/biology/infernal/infernal-1.1.3/src/impl_sse/
H A D	cmsearch_dual	`31 $fafile = $ARGV[1]; 41 $tbl_out .= $fafile; 47 …"-Z $opt_Z":'', "--noali", "--tblout $tbl_out", $cmsearch_options, $cmfile, $fafile, "> $logfile"); 82 @args = ($sse_cmsearch, $opt_Z?"-Z $opt_Z":'', "--glbf 3", $sse_cmsearch_options, $cmfile, $fafile,… 112 unless (-e "$fafile\.ssi") { 113 system("$sfetch --index $fafile"); 117 @args = ($sfetch, "-c",$href->{start}.'\.\.'.$href->{stop}, $fafile, $href->{seq}, ">> $fa2");`
/dports/biology/infernal/infernal-1.1.3/hmmer/profmark/
H A D	x-iterate-jackhmmer	`13 $fafile = shift; 28 if (! -e "$fafile.iter") { die "iteration db $fafile.iter doesn't exist"; } 45 …$cmd = "$jackhmmer $iteropts -A $wrkdir/$msaname.jck $wrkdir/$msaname.query $fafile.iter > /dev/nu… 47 …$cmd = "$hmmsearch $searchopts --tblout $wrkdir/$msaname.tmp $wrkdir/$msaname.hmm $fafile > /dev/n…`
H A D	x-hmmsearch	`20 $fafile = shift; 47 …msearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > /dev/null"); 48 …FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile"; }`
H A D	x-hmmsearch-max	`20 $fafile = shift; 47 …msearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > /dev/null"); 48 …FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile"; }`
H A D	x-phmmer-consensus	20 $fafile = shift; 47 …r $opts --cpu 1 --tblout $resultdir/$msaname.tmp $resultdir/$msaname.query.fa $fafile > /dev/null`; 48 …ie "FAILED: $phmmer --tblout $resultdir/$msaname.tmp $opts $resultdir/$msaname.query.fa $fafile"; }
H A D	x-h2-fs	`20 $fafile = shift; 56 if (! open(HMMSEARCH, "$hmmsearch $searchopts $resultdir/$msaname.hmm $fafile 2> /dev/null \|")) 57 { print "FAILED: $hmmsearch $searchopts $resultdir/$msaname.hmm $fafile\n"; next MSA; }`
H A D	x-h2-ls	`20 $fafile = shift; 56 if (! open(HMMSEARCH, "$hmmsearch $searchopts $resultdir/$msaname.hmm $fafile 2> /dev/null \|")) 57 { print "FAILED: $hmmsearch $searchopts $resultdir/$msaname.hmm $fafile\n"; next MSA; }`
H A D	x-fps-phmmer	21 $fafile = shift; 60 …`$phmmer --cpu 1 --tblout $wrkdir/$msaname.tmp $opts $wrkdir/$msaname.query.fa $fafile > /dev/null… 61 …if ($?) { print "FAILED: $phmmer --tblout $msaname.tmp $opts $wrkdir/$msaname.query.fa $fafile\n";…
H A D	x-iterate-psiblast	`9 $fafile = shift; 55 …$cmd = "$blastpgp $blastopts1 -d $fafile.iter -i $wrkdir/$msaname.query -C $wrkdir/$msaname.asnt"… 56 …$cmd = "$blastpgp $blastopts2 -d $fafile -R $wrkdir/$msaname.asnt 2>/dev/null \|"; …`
/dports/biology/hmmer/hmmer-3.3/profmark/
H A D	x-iterate-jackhmmer	`13 $fafile = shift; 28 if (! -e "$fafile.iter") { die "iteration db $fafile.iter doesn't exist"; } 45 …$cmd = "$jackhmmer $iteropts -A $wrkdir/$msaname.jck $wrkdir/$msaname.query $fafile.iter > /dev/nu… 47 …$cmd = "$hmmsearch $searchopts --tblout $wrkdir/$msaname.tmp $wrkdir/$msaname.hmm $fafile > /dev/n…`
H A D	x-hmmsearch	`20 $fafile = shift; 47 …msearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > /dev/null"); 48 …FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile"; }`
H A D	x-hmmsearch-max	`20 $fafile = shift; 47 …msearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > /dev/null"); 48 …FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile"; }`
H A D	x-phmmer-consensus	20 $fafile = shift; 47 …r $opts --cpu 1 --tblout $resultdir/$msaname.tmp $resultdir/$msaname.query.fa $fafile > /dev/null`; 48 …ie "FAILED: $phmmer --tblout $resultdir/$msaname.tmp $opts $resultdir/$msaname.query.fa $fafile"; }
H A D	x-h2-fs	`20 $fafile = shift; 56 if (! open(HMMSEARCH, "$hmmsearch $searchopts $resultdir/$msaname.hmm $fafile 2> /dev/null \|")) 57 { print "FAILED: $hmmsearch $searchopts $resultdir/$msaname.hmm $fafile\n"; next MSA; }`
H A D	x-h2-ls	`20 $fafile = shift; 56 if (! open(HMMSEARCH, "$hmmsearch $searchopts $resultdir/$msaname.hmm $fafile 2> /dev/null \|")) 57 { print "FAILED: $hmmsearch $searchopts $resultdir/$msaname.hmm $fafile\n"; next MSA; }`

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