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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 $file |
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$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, $dbfile)=@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 blat's protein-to-dnax mode; |
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Never use without a parent controllers (e.g. gridx). |
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Usage example: |
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gridx -g condor -p 20 -n 2000 -i proteins.fa blat_prot.psx /fs/fullpath/to/dna_db.fa |
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}; #' |
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|
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die $usage."\n" unless -s $file && $total && $dbfile; |
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my $fout=$file.'.gff3'; |
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|
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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 $toskip=($file =~ m/_\@(\d+)_v\d+\.\d+/) ? $1 : $skipped+$numpass*($slice_num-1); |
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#my ($srvhost, $srvport)=split(/\:/,$srv); |
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#$srvport=8080 unless $srvport; |
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my $cmd="gblat -minScore=50 -minIdentity=70 -t=dnax -q=prot -out=gff -noHead $dbfile $file $fout"; |
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|
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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, $fout); |
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|
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print STDERR "<<$slno: done.\n"; |
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unlink($file); |
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exit 0; |
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|
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sub runCmd { |
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my ($docmd, @todel) = @_; |
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my $errmsg = `($docmd) 2>&1`; |
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if ($? || ($errmsg=~/ERROR/si) || ($errmsg=~/Segmentation/si) || ($errmsg=~/Failed/s) || $errmsg=~/Invalid/s) { |
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print STDERR "!Error at:\n$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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} |
