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gpertea |
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#!/usr/bin/perl |
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use strict; |
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use FindBin; |
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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 $file |
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$ENV{'PATH'}=$FindBin::Bin.':'.$ENV{'PATH'}; |
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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, $gfa)=@ARGV; |
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#print STDERR "running: $0 ".join(' ',@ARGV)."\n"; |
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my $usage=q{ |
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Slice processing script for exonerate protein2dna model client option |
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Never use without a parent controllers (e.g. gridx). |
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Must start the server prior to running this gridx command. |
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Usage example: |
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gridx -q -N -O logs -g condor -p 20 -n 3000 -i proteindb.fa exonerate_p2g.psx /full/path/to/genomicDNA.fa |
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}; |
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die $usage."\n (genome file='$gfa', qslice='$file')\n" unless (-f $gfa) && (-s $file); |
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my $fout=$file.'.gff3'; |
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my $fexout=$file.'.exo'; |
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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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my $cmd="exonerate.icc $file $gfa -V 0 --model p2g --percent 20 -n 11 --showalignment no --saturatethreshold 80 ". |
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"--ryo '".'%ti\t%qi\tmap_end\t%r\t%ql|%qab-%qae\t%ps\t%g\t%qd\n'."' --geneseed 60 -x 50 --proteinwordlen 4 ". |
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"--seedrepeat 2 --maxintron 400000 -M 512 --showtargetgff yes --showvulgar no > $fexout"; |
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#my $cmd="gmap -D $dbdir -d $gmapdb -B 2 -f 1 $file > $gmap_res"; |
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my $slno=sprintf("slice:%09d",$slice_num); |
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print STDERR ">>$slno: $cmd\n"; |
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&runCmd($cmd, $fexout); |
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if (-s $fexout) { |
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$cmd="fltexonerate -p70 -c70 < $fexout > $fout"; |
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&runCmd($cmd, $fout); |
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} |
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print STDERR "<<$slno: done.\n"; |
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unlink($file); |
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exit 0; |
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sub runCmd { |
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my ($docmd, @todel) = @_; |
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my $errmsg = `( $docmd ) 2>&1`; |
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my $errcode=$?; |
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my @cores=<core.*>; |
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if ($errcode || @cores>0 || ($errmsg=~/error|segmentation|violation/si) || ($errmsg=~/\bfail/si)) { |
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print STDERR "!Error at:\n$docmd\n"; |
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print STDERR "$errmsg\n"; |
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foreach (@todel) { |
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unlink($_); |
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} |
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exit(1); |
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} |
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} |
