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
|
#!/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\n\n";
my $sam_file = $ARGV[0] or die $usage;
main: {
my $sam_reader = new SAM_reader($sam_file);
while (my $sam_entry = $sam_reader->get_next()) {
my $read_name = $sam_entry->reconstruct_full_read_name();
my $sequence = $sam_entry->get_sequence();
if ((! $sam_entry->is_query_unmapped()) && $sam_entry->get_query_strand() eq '-') {
$sequence = &reverse_complement($sequence);
}
print ">$read_name\n$sequence\n";
}
exit(0);
}
|
