1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
|
#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 genome_db transcript_db maxIntron outFile\n\n";
my $genome_db = $ARGV[0] or die $usage;
my $transcript_db = $ARGV[1] or die $usage;
my $max_intron = $ARGV[2] or die $usage;
my $outFile = $ARGV[3] or die $usage;
main: {
my $ooc_cmd = "blat -t=dna -q=rna -maxIntron=$max_intron -makeOoc=11.ooc $genome_db $transcript_db $outFile";
unless (-s "11.ooc") {
&process_cmd($ooc_cmd);
}
my $blat_cmd = "blat -t=dna -q=rna -maxIntron=$max_intron -ooc=11.ooc $genome_db $transcript_db $outFile";
&process_cmd($blat_cmd);
exit(0);
}
sub process_cmd {
my ($cmd) = @_;
my $ret = system($cmd);
if ($ret) {
die "Error, $cmd died with ret $ret";
}
return;
}
|
