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|
#!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################
#
# Required:
# --genome <string> target genome to align to
# and
# --reads <string> fastq files. If pairs, indicate both in quotes, ie. "left.fq right.fq"
# or
# --samples_file <string> samples.txt file (format: sample_name(tab)left.fq(tab)right.fq)
# Optional:
# -N <int> number of top hits (default: 1)
# -I <int> max intron length (default: 1000000)
# -G <string> GTF file for incorporating reference splice site info.
# --CPU <int> number of threads (default: 2)
# --out_prefix <string> output prefix (default: gsnap)
# --no_sarray skip the sarray in the gmap-build
# --proper_pairs_only require proper pairing of reads
#
#######################################################################
__EOUSAGE__
;
my ($genome, $reads);
my $max_intron = 1000000;
my $CPU = 2;
my $help_flag;
my $num_top_hits = 1;
my $out_prefix = "gsnap";
my $gtf_file;
my $no_sarray = "";
my $proper_pairs_only_flag = 0;
my $samples_file;
&GetOptions( 'h' => \$help_flag,
'genome=s' => \$genome,
'reads=s' => \$reads,
'I=i' => \$max_intron,
'CPU=i' => \$CPU,
'N=i' => \$num_top_hits,
'out_prefix=s' => \$out_prefix,
'G=s' => \$gtf_file,
'no_sarray' => \$no_sarray,
'proper_pairs_only' => \$proper_pairs_only_flag,
'samples_file=s' => \$samples_file,
);
unless ($genome && ($reads || $samples_file)) {
die $usage;
}
if ($no_sarray) {
$no_sarray = "--no-sarray";
}
main: {
my $genomeName = basename($genome);
my $genomeDir = $genomeName . ".gmap";
my $genomeBaseDir = dirname($genome);
my $cwd = cwd();
unless (-d "$genomeBaseDir/$genomeDir") {
my $cmd = "gmap_build -D $genomeBaseDir -d $genomeDir -T $genomeBaseDir -k 13 $no_sarray $genome >&2";
&process_cmd($cmd);
}
my $splice_file;
my $splice_param = "";
if ($gtf_file) {
$splice_file = "$gtf_file.gsnap.splice";
if (! -s $splice_file) {
# create one.
my $cmd = "gtf_splicesites < $gtf_file > $splice_file";
&process_cmd($cmd);
$cmd = "iit_store -o $splice_file.iit < $splice_file";
&process_cmd($cmd);
}
$splice_param = "--use-splicing=$splice_file.iit";
}
## run GMAP
my $gsnap_use_sarray = ($no_sarray) ? "--use-sarray=0" : "";
my @reads_files;
if ($samples_file) {
open (my $fh, $samples_file) or die $!;
while (<$fh>) {
chomp;
my ($condition, $sample_name, @read_paths) = split(/\s+/);
my $read_paths_str = join(" ", @read_paths);
push (@reads_files, [$sample_name, $read_paths_str]);
}
close $fh;
}
else {
@reads_files = [$out_prefix, $reads];
}
foreach my $read_set_aref (@reads_files) {
my ($out_prefix, $reads) = @$read_set_aref;
if ($reads =~ /\.gz$/) {
$reads .= " --gunzip";
}
my $require_proper_pairs = "";
if ($proper_pairs_only_flag) {
$require_proper_pairs = " -f 2 ";
}
my $cmd = "bash -c \"set -o pipefail && gsnap -D $genomeBaseDir -d $genomeDir -A sam -N 1 -w $max_intron $gsnap_use_sarray -n $num_top_hits -t $CPU $reads $splice_param @ARGV | samtools view -bS -F 4 $require_proper_pairs - | samtools sort -@ $CPU - -o $out_prefix.cSorted.bam \"";
&process_cmd($cmd);
if (-s "$out_prefix.cSorted.bam") {
$cmd = "samtools index $out_prefix.cSorted.bam";
&process_cmd($cmd);
}
}
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
#return;
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret ($ret)";
}
return;
}
|
