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
37
38
39
40
41
42
43
44
45
46
47
|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "usage: $0 alignments.sam SS_lib_type=F,R,FR,RF\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $SS_lib_type = $ARGV[1] or die $usage;
unless ($SS_lib_type =~ /^(F|R|FR|RF)$/) {
die $usage;
}
main: {
my $sam_reader = new SAM_reader($sam_file);
open (my $plus_ofh, ">$sam_file.+.sam") or die "Error, cannot write to $sam_file.+.sam";
open (my $minus_ofh, ">$sam_file.-.sam") or die "Error, cannot write to $sam_file.-.sam";
while (my $sam_entry = $sam_reader->get_next()) {
if ($sam_entry->is_query_unmapped()) {
next;
}
my $transcribed_strand = $sam_entry->get_query_transcribed_strand($SS_lib_type);
my $ofh = ($transcribed_strand eq '+') ? $plus_ofh : $minus_ofh;
print $ofh $sam_entry->toString() . "\n";
}
close $plus_ofh;
close $minus_ofh;
exit(0);
}
|
