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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use SAM_reader;
use SAM_entry;
use Nuc_translator;
my $usage = "usage: $0 file.sam out_prefix\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $out_prefix = $ARGV[1] or die $usage;
main: {
my $sam_reader = new SAM_reader($sam_file);
my %fhs;
while (my $sam_entry = $sam_reader->get_next()) {
if ($sam_entry->is_query_unmapped()) {
next;
}
my $outfh = &get_output_file($sam_entry, \%fhs);
my $seq = $sam_entry->get_sequence();
my $quals = $sam_entry->get_quality_scores();
my $strand = $sam_entry->get_query_strand();
if ($strand eq '-') {
$seq = &reverse_complement($seq);
$quals = join("", reverse(split(//, $quals)));
}
my $read_name = $sam_entry->reconstruct_full_read_name();
print $outfh join("\n", "\@$read_name", $seq, "+", $quals) . "\n";
}
exit(0);
}
####
sub get_output_file {
my ($sam_entry, $fhs_href) = @_;
my $filename = "$out_prefix.single.fq";
if ($sam_entry->is_paired()) {
if ($sam_entry->is_first_in_pair()) {
$filename = "$out_prefix.left.fq";
}
elsif ($sam_entry->is_second_in_pair()) {
$filename = "$out_prefix.right.fq";
}
else {
die "Error, read is paired but neither first or second in pair!";
}
}
my $fh = $fhs_href->{$filename};
unless ($fh) {
open ($fh, ">$filename") or die "Error, cannot write to $filename";
$fhs_href->{$filename} = $fh;
}
return($fh);
}
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