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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 $usage = <<__EOUSAGE__;
######################################################################
#
# Required:
# --genome <string> target genome to align to
# --transcripts <string> cdna sequences to align
#
# Optional:
# -N <int> number of top hits (default: 1)
# -I <int> max intron length
# --CPU <int> number of threads (default: 2)
# --no_chimera do not report chimeric alignmetnts
# --SAM output in SAM format
# --gtf <string> gene structure annotations in gtf format (for genome building)
# --splice_assist <string> splice assist mode (introns or splicesites)
#
#
#######################################################################
__EOUSAGE__
;
my ($genome, $transcriptDB, $max_intron);
my $CPU = 2;
my $help_flag;
my $number_top_hits = 1;
my $no_chimera_flag = 0;
my $SAM_flag = 0;
my $gtf_file = 0;
my $splice_assist = "";
&GetOptions( 'h' => \$help_flag,
'genome=s' => \$genome,
'transcripts=s' => \$transcriptDB,
'I=i' => \$max_intron,
'CPU=i' => \$CPU,
'N=i' => \$number_top_hits,
'no_chimera' => \$no_chimera_flag,
'SAM' => \$SAM_flag,
'gtf=s' => \$gtf_file,
'splice_assist=s' => \$splice_assist,
);
if ($help_flag) {
die $usage;
}
unless ($genome && $transcriptDB) {
die $usage;
}
if ($splice_assist) {
unless ($splice_assist =~ /^(introns|splicesites)$/) {
die "Error, splice_assist $splice_assist not recognized as an option";
}
}
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 $genomeBaseDir/$genomeDir -k 13 $genome >&2";
my $cmd = "gmap_build -D $genomeBaseDir -d $genomeDir -k 13 $genome >&2";
&process_cmd($cmd);
if ($gtf_file) {
&build_intron_n_splice_info_files($genomeBaseDir, $genomeDir, $gtf_file);
}
}
## run GMAP
my $num_gmap_top_hits = $number_top_hits;
if ((! $no_chimera_flag) && $num_gmap_top_hits == 1) {
$num_gmap_top_hits = 0; # reports two hits if chimera with this setting.
}
my $format = ($SAM_flag) ? "samse" : "3";
my $cmd = "gmap -D $genomeBaseDir -d $genomeDir $transcriptDB -f $format -n $num_gmap_top_hits -x 50 -t $CPU -B 5 ";
if ($max_intron) {
$cmd .= " --intronlength=$max_intron ";
}
if ($splice_assist) {
$cmd .= " -m ref_${splice_assist}.iit";
}
&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;
}
####
sub build_intron_n_splice_info_files {
my ($genomeBaseDir, $genomeDir, $gtf_file) = @_;
my $genome_maps_dir = "$genomeBaseDir/$genomeDir/$genomeDir.maps";
my $introns_iit_file = "$genome_maps_dir/ref_introns.iit";
my $cmd = "gtf_introns < $gtf_file | iit_store -o $introns_iit_file";
&process_cmd($cmd);
if (! -e $introns_iit_file) {
die "Error, no introns $introns_iit_file";
}
my $splicesites_iit_file = "$genome_maps_dir/ref_splicesites.iit";
$cmd = "gtf_splicesites < $gtf_file | iit_store -o $splicesites_iit_file";
&process_cmd($cmd);
if (! -e $splicesites_iit_file) {
die "Error, no splicesites $splicesites_iit_file";
}
return;
}
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