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#!/usr/bin/perl |
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use strict; |
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umask 0002; |
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my $usage=q{ |
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gridx/psx slice processing script for pfam - never to be used by itself. |
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|
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Usage: |
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|
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gridx [gridx_opts] -i <proteinfile> pfam_slice.psx <pfam_domains_dir> \ |
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[pfam_scan.pl_options] |
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|
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Example: |
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|
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gridx -p 20 -n 1000 -m gpertea -q -i tranprots.fa pfam_slice.psx \ |
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/fs/szgenefinding/domains/pfam --fast |
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|
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(searching 1000 proteins at a time from input file tranprots.fa, |
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using at most 20 cpus on the grid; notify user gpertea by e-mail |
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when finished) |
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}; |
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|
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# 1 is the name of the slice file |
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# 2 is the # of sequences in the slice file |
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# 3 is the slice# being processed (1-based) |
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# 4 is 1 if this is the last slice, 0 if not the last slice |
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# 5 is the # of sequences skipped initially |
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# 6 is the upper limit of slices to be processed (-1 = ALL) |
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# 7.. user parameters |
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# 1 2 3 4 5 6 7 ... |
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my ($file, $numpass, $slice_num, $last, $skipped, $total, $pfamdir, @otheropts)=@ARGV; |
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|
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die "$usage\n" unless -d $pfamdir; |
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|
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my $log_file='log_std'; |
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my $err_file='err_log'; |
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# -- redirect output just in case.. |
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open(STDERR, '>>'.$err_file); |
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open(STDOUT, '>>'.$log_file); |
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|
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my $pfam_res=$file.'.pfam'; |
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my $pfamopts=join(' ',@otheropts); |
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my $cmd="/fs/szannotation/bin/pfam_scan.pl $pfamopts -d $pfamdir". |
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" -o $pfam_res $file"; |
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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, $pfam_res); |
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print STDERR "<<$slno: done.\n"; |
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|
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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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} |
