89 lines
1.8 KiB
Perl
89 lines
1.8 KiB
Perl
#!/usr/bin/env perl
|
|
|
|
use strict;
|
|
use warnings;
|
|
use FindBin;
|
|
use lib ("$FindBin::Bin/../../PerlLib");
|
|
use Process_cmd;
|
|
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
|
|
use Carp;
|
|
|
|
|
|
my $CPU = 2;
|
|
|
|
my $usage = <<__EOUSAGE__;
|
|
|
|
############################################################################
|
|
#
|
|
# --target <string> target for alignment
|
|
#
|
|
# --left <string> read_1.fq
|
|
#
|
|
# optional:
|
|
#
|
|
# --right <string> read_2.fq
|
|
#
|
|
# --CPU <int> number of threads (default: $CPU)
|
|
#
|
|
# --max_hits <int> default 10
|
|
|
|
usage: $0 --target target.seq --left reads_1.fq [--right reads_2.fq --CPU 8]
|
|
|
|
and you can pipe it into samtools to make a bam file:
|
|
|
|
| samtools view -@ 8 -Sb - | samtools sort -@ 8 -m 4G - -o bowtie2.coordSorted.bam
|
|
|
|
#############################################################################
|
|
|
|
|
|
|
|
__EOUSAGE__
|
|
|
|
;
|
|
|
|
|
|
my $help_flag;
|
|
my $target_seq;
|
|
my $reads_1_fq;
|
|
my $reads_2_fq;
|
|
my $max_hits = 10;
|
|
|
|
&GetOptions ( 'h' => \$help_flag,
|
|
'target=s' => \$target_seq,
|
|
'left=s' => \$reads_1_fq,
|
|
'right=s' => \$reads_2_fq,
|
|
'CPU=i' => \$CPU,
|
|
'max_hits=i' => \$max_hits,
|
|
);
|
|
|
|
|
|
if ($help_flag) { die $usage; }
|
|
|
|
unless ($target_seq && $reads_1_fq) { die $usage; }
|
|
|
|
|
|
|
|
main: {
|
|
|
|
unless (-s "$target_seq.1.bt2") {
|
|
my $cmd = "bowtie2-build $target_seq $target_seq 1>&2 ";
|
|
&process_cmd($cmd);
|
|
}
|
|
|
|
my $format = ($reads_1_fq =~ /\.fq|\.fastq/) ? "-q" : "-f";
|
|
|
|
my $bowtie2_cmd = "bowtie2 --threads $CPU --local --no-unal -x $target_seq $format -k $max_hits";
|
|
if ($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);
|
|
}
|
|
|