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
|
#!/usr/bin/env perl
use strict;
use warnings;
use Findbin;
use lib ("$FindBin::Bin/../../PerlLib");
use Process_cmd;
my $usage = "usage: $0 target.seq reads_1.fq [reads_2.fq]\n\n"
. " and you can pipe it into samtools to make a bam file:\n\n"
. "\t | samtools view -Sb - | samtools sort - myoutputbamMinusExtension\n\n";
my $target_seq = $ARGV[0] or die $usage;
my $reads_1_fq = $ARGV[1] or die $usage;
my $reads_2_fq = $ARGV[2];
main: {
unless (-s "$target_seq.1.bt2") {
my $cmd = "bowtie2-build $target_seq $target_seq 1>&2 ";
&process_cmd($cmd);
}
my $format = ($reads_1_fq =~ /\.fq/) ? "-q" : "-f";
my $bowtie2_cmd = "bowtie2 --local --no-unal -x $target_seq $format ";
if ($reads_2_fq) {
$bowtie2_cmd .= " -1 $reads_1_fq -2 $reads_2_fq ";
}
else {
$bowtie2_cmd .= " -U $reads_1_fq ";
}
&process_cmd($bowtie2_cmd);
exit(0);
}
|
