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#!/usr/bin/perl |
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use strict; |
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use FindBin; |
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|
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umask 0002; |
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#the line below is needed if pvmsx is used |
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# also, the error condition is set only by the presence of $file |
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chdir($ENV{PVMSX_WD}) if ($ENV{PVMSX_WD}); |
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|
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|
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$ENV{'PATH'}=$FindBin::Bin.':'.$ENV{'PATH'}; |
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|
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#so for pvmsx to consider the task was successful, $file must be deleted! |
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#============== |
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# 1 is the name of the fasta sequence input file |
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# 2 is the # of sequences in ${1} should = 1 for this script |
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# 3 is the slice no. being processed by sx |
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# 4 is 0 if not the last file, 1 if the last file |
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# 5 is the # of sequences skipped initially |
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# 6 is the # of sequences to be processed (-1 = ALL) |
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# 7 user parameter |
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# 1 2 3 4 5 6 |
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my ($file, $numpass, $slice_num, $last, $skipped, $total, $userparams)=@ARGV; |
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#user parameters: |
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# 1) database (full path) |
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# 2) PID cutoff (using 94 if not specified) |
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# 3) maximum overhang |
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# 4) minimum overlap |
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# 5) extra flags (optional) |
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# flags: M = no masking, D= separate database (not all-vs-all) |
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# G = show gaps |
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my ($searchdb,$pid,$maxovh,$minovl, $xflags)=split(/:/,$userparams); |
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my $blast_res=$file.'.tab'; |
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my $nomasking = $xflags=~/M/; |
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my $gapinfo = $xflags=~/G/; |
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my $otherDb = $xflags=~/D/; |
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|
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$pid=25 unless $pid>20; #not used for this tblastx search |
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$minovl=40 unless $minovl; #not used for this blastn |
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my $log_file='log_std'; |
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my $err_file='err_log'; |
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open(STDERR, '>>'.$err_file); |
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open(STDOUT, '>>'.$log_file); |
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|
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my $toskip = $skipped+$numpass*($slice_num-1); |
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$ENV{BLASTMAT}='/fs/sz-user-supported/Linux-i686/packages/wu-blast/matrix'; |
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my $cmd = "tblastx $searchdb $file E=1e-10 B=300000 V=300000 -noseqs -notes -warnings -novalidctxok -cpus=1 -topcomboN 1 "; |
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$cmd.= " -dbrecmin $toskip " if $toskip>0 && $otherDb==0; |
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# $cmd.= "| blastflt PID=25 | bzip2 -cf > $blast_res.bz2"; |
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$cmd.= "| blast2btab PID=25 | bzip2 -f > $blast_res.bz2" ; |
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# $cmd.=$gapinfo ? ' -D5 ':' -D4 '; |
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# $cmd.= ($nomasking) ? ' -FF -UF ' : ' -UT -F "m D" '; |
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# unless ($otherDb) { |
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# $cmd.=' -KT '; |
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# $cmd.= " -k $toskip " if $toskip>0; |
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# } |
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#$cmd.=" > $blast_res"; |
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my $slno=sprintf("slice:%09d",$slice_num); |
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print STDERR ">>$slno: $cmd\n"; |
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|
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my $errmsg = `($cmd) 2>&1`; |
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my $r=$?; |
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print STDERR "<<$slno: done.\n"; |
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|
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if ($r || ($errmsg=~/ERROR/is) || ($errmsg=~/Segmentation/is)) { |
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print STDERR "!Error at:\n$cmd\n"; |
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print STDERR "$errmsg\n"; |
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exit(1); |
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} |
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#------- sorting of results not needed for blastn |
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# $cmd="sort -k11,11g -k10,10nr -k9,9nr $blast_res | bzip2 -cf > $mgblast_res.bz2"; |
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# $errmsg=`($cmd) 2>&1`; |
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#$r=$?; |
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#if (($r && ($r>>8 != 2)) || $errmsg=~m/memory/is) { |
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# die "Error sorting/compressing the results file '$mgblast_res'\n$cmd\n"; |
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# } |
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# unlink($file, $mgblast_res); |
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unlink($file); |
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exit 0; |
