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root/gclib/scripts/blat_protdb.psx
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 1 month ago) by gpertea
File size: 2029 byte(s)
Log Message:
Line File contents
1 #!/usr/bin/perl
2 use strict;
3 use FindBin;
4
5 umask 0002;
6 #the line below is needed if pvmsx is used
7 # also, the error condition is set only by the presence of $file
8 $ENV{'PATH'}=$FindBin::Bin.':'.$ENV{'PATH'};
9
10 #so for pvmsx to consider the task was successful, $file must be deleted!
11 #==============
12 # 1 is the name of the fasta sequence input file
13 # 2 is the # of sequences in ${1} should = 1 for this script
14 # 3 is the slice no. being processed by sx
15 # 4 is 0 if not the last file, 1 if the last file
16 # 5 is the # of sequences skipped initially
17 # 6 is the # of sequences to be processed (-1 = ALL)
18 # 7 user parameter
19 # 1 2 3 4 5 6
20 my ($file, $numpass, $slice_num, $last, $skipped, $total, $prots)=@ARGV;
21 #print STDERR "running: $0 ".join(' ',@ARGV)."\n";
22 my $usage=q{
23 Slice processing script for blat's protein-to-dnax mode;
24 Never use without a parent controllers (e.g. gridx).
25 Usage example:
26 gridx -q -N -O logs -g condor -p 20 -n 2000 -i contigdb.fa blat_protdb.psx /fs/fullpath/to/proteins.fa
27 }; #'
28
29 die $usage."\n" unless -s $file && $total && $prots;
30 my $fout=$file.'.gff3';
31
32 my $log_file='log_std';
33 my $err_file='err_log';
34 open(STDERR, '>>'.$err_file);
35 open(STDOUT, '>>'.$log_file);
36
37 #my $toskip=($file =~ m/_\@(\d+)_v\d+\.\d+/) ? $1 : $skipped+$numpass*($slice_num-1);
38 #my ($srvhost, $srvport)=split(/\:/,$srv);
39 #$srvport=8080 unless $srvport;
40 my $cmd="gblat -minScore=50 -minIdentity=70 -t=dnax -q=prot -out=gff -noHead $file $prots $fout";
41
42 #my $cmd="gmap -D $dbdir -d $gmapdb -B 2 -f 1 $file > $gmap_res";
43 my $slno=sprintf("slice:%09d",$slice_num);
44 print STDERR ">>$slno: $cmd\n";
45 &runCmd($cmd, $fout);
46
47 print STDERR "<<$slno: done.\n";
48 unlink($file);
49 exit 0;
50
51 sub runCmd {
52 my ($docmd, @todel) = @_;
53 my $errmsg = `($docmd) 2>&1`;
54 if ($? || ($errmsg=~/ERROR/si) || ($errmsg=~/Segmentation/si) || ($errmsg=~/Failed/s) || $errmsg=~/Invalid/s) {
55 print STDERR "!Error at:\n$docmd\n";
56 print STDERR "$errmsg\n";
57 foreach (@todel) {
58 unlink($_);
59 }
60 exit(1);
61 }
62 }

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