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root/gclib/scripts/blat_client.psx
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 1 month ago) by gpertea
File size: 2263 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, $serverport, $dbdir)=@ARGV;
21 #print STDERR "running: $0 ".join(' ',@ARGV)."\n";
22 my $usage=q{
23 Slice processing script for blat protein-to-dnax mode;
24 Never use without a parent controllers (e.g. gridx).
25 Must start the server prior to running this gridx command.
26 Usage example:
27 gridx -q -N -O logs -g condor -p 20 -n 2000 -i proteins.fa blat_client.psx server:port /fullpath/to/dbseqdir
28 };
29
30 die $usage."\n" unless -s $file && $total && $dbdir;
31 my $fout=$file.'.gff3';
32 my ($server, $port)=split(/:/, $serverport);
33 die $usage."\n" unless $port>255;
34 die $usage."\nInvalid data directory $dbdir" unless -d $dbdir;
35 my $log_file='log_std';
36 my $err_file='err_log';
37 open(STDERR, '>>'.$err_file);
38 open(STDOUT, '>>'.$log_file);
39
40 #my $toskip=($file =~ m/_\@(\d+)_v\d+\.\d+/) ? $1 : $skipped+$numpass*($slice_num-1);
41 #my ($srvhost, $srvport)=split(/\:/,$srv);
42 #$srvport=8080 unless $srvport;
43 my $cmd="gfClient -minScore=50 -minIdentity=70 -t=dnax -q=prot -out=gff -nohead $server $port $dbdir $file $fout";
44
45 #my $cmd="gmap -D $dbdir -d $gmapdb -B 2 -f 1 $file > $gmap_res";
46 my $slno=sprintf("slice:%09d",$slice_num);
47 print STDERR ">>$slno: $cmd\n";
48 &runCmd($cmd, $fout);
49
50 print STDERR "<<$slno: done.\n";
51 unlink($file);
52 exit 0;
53
54 sub runCmd {
55 my ($docmd, @todel) = @_;
56 my $errmsg = `($docmd) 2>&1`;
57 if ($? || ($errmsg =~ m/Error|Segmentation|Failed|Invalid/is)) {
58 print STDERR "!Error at:\n$docmd\n";
59 print STDERR "$errmsg\n";
60 system("cp $file err.at.$file");
61 foreach (@todel) {
62 unlink($_);
63 }
64 # exit(1);
65 return 0;
66 }
67 }

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svn:executable *