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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 genes.fasta transcripts.fasta max_intron BLAT_CPU [STRAND-SPECIFIC_FLAG=0]\n\n";
my $genes_fasta = $ARGV[0] or die $usage;
my $trans_fasta = $ARGV[1] or die $usage;
my $max_intron = $ARGV[2] or die $usage;
my $blat_cpu = $ARGV[3] or die $usage;
my $SS = $ARGV[4] || 0;
main: {
## run blat:
my $cmd = "/usr/lib/trinityrnaseq/util/misc/blat_util/process_BLAT_alignments.pl -g $genes_fasta -t $trans_fasta -I $max_intron --CPU $blat_cpu --KEEP_PSLX";
&process_cmd($cmd);
$cmd = "cat blat_out_dir/*top_1 > blat.top_1.pslx";
&process_cmd($cmd);
$cmd = "/usr/lib/trinityrnaseq/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl blat.top_1.pslx $SS";
&process_cmd($cmd);
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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