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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 genome.fasta left.fq right.fq [output_dir]\n\n";
my $genome_file = $ARGV[0] or die $usage;
my $left_fq_file = $ARGV[1] or die $usage;
my $right_fq_file = $ARGV[2] or die $usage;
my $output_dir = $ARGV[3] || "bowtie.$$.dir";
while ($output_dir =~ m|/$|) {
chop $output_dir;
}
main: {
## run bowtie
my $cmd = "$FindBin::RealBin/../alignReads.pl --target $genome_file --left $left_fq_file --right $right_fq_file "
. " --seqType fq --aligner bowtie -o $output_dir --max_dist_between_pairs 900000000 --no_rsem --retain_intermediate_files "
. " -- -a -m 1 --best --strata -p 4 --chunkmbs 512 ";
&process_cmd($cmd) unless (-s "$output_dir/$output_dir.nameSorted.sam");
$cmd = "/usr/lib/trinityrnaseq/util/misc/HiCpipe_nameSortedSam_to_raw.pl $output_dir/$output_dir.nameSorted.sam > $output_dir/$output_dir.raw";
&process_cmd($cmd) unless (-s "$output_dir/$output_dir.raw");
exit(0);
}
####
sub process_cmd {
my ($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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