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|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib("$FindBin::RealBin/../../PerlLib");
use Pipeliner;
use File::Basename;
use Cwd;
use List::Util qw(min);
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################
#
# Required:
# --bam_file_list <string> bam_file_list (format: sample_id(tab)/path/to/file.bam)
#
# Optional
# --gtf <string> annotations in gtf format
# --CPU <int> number of threads (default: 2)
# --SS_lib_type <string>
#
#
#######################################################################
__EOUSAGE__
;
my $bam_file_list;
my $CPU = 2;
my $help_flag;
my $gtf_file;
my $SS_lib_type;
&GetOptions( 'h' => \$help_flag,
'bam_file_list=s' => \$bam_file_list,
'CPU=i' => \$CPU,
'gtf=s' => \$gtf_file,
'SS_lib_type=s' => \$SS_lib_type,
);
unless ($bam_file_list) {
die $usage;
}
if ($help_flag) {
die $usage;
}
if (@ARGV) {
die "Error, cannot recognize opts: @ARGV";
}
main: {
## ensure all full paths
$gtf_file = &Pipeliner::ensure_full_path($gtf_file) if $gtf_file;
my @entries;
open(my $fh, $bam_file_list) or die $!;
while(<$fh>) {
chomp;
my ($sample_id, $bam_filename) = split(/\t/);
unless ($sample_id && $bam_filename) {
die "Error, bam file list doesn't have expected tab-delimited formatting at $_";
}
unless (-e $bam_filename) {
die "Error, cannot locate file: $bam_filename";
}
push (@entries, { sample_id => $sample_id,
bam => $bam_filename } );
}
my $pipeliner = new Pipeliner(-verbose => 1);
my @indiv_stringtie_outputs;
foreach my $entry (@entries) {
my $cmd = "stringtie " . $entry->{bam} .
" -l STRG." . $entry->{sample_id} . " ";
if ($SS_lib_type) {
if ($SS_lib_type =~ /^R/i) {
$cmd .= " --rf ";
}
elsif ($SS_lib_type =~ /^F/i) {
$cmd .= " --fr ";
}
else {
die "Error, cannot determine strand-specificity type from $SS_lib_type";
}
}
$cmd .= " -o " . $entry->{sample_id} . ".strg.gtf";
push (@indiv_stringtie_outputs, $entry->{sample_id} . ".strg.gtf");
if ($gtf_file) {
$cmd .= " -G $gtf_file ";
}
my $checkpoint = $entry->{sample_id} . ".strg.ok";
$pipeliner->add_commands( new Command($cmd, $checkpoint));
}
$pipeliner->run();
# merge transcripts
if (scalar(@indiv_stringtie_outputs) > 1) {
my $cmd = "stringtie --merge -o stringtie.merged.gtf -g 1 ";
if ($gtf_file) {
$cmd .= " -G $gtf_file ";
}
$cmd .= join(" ", @indiv_stringtie_outputs);
$pipeliner->add_commands( new Command($cmd, "stringtie_merge.ok"));
$pipeliner->run();
}
exit(0);
}
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