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#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $help_flag;
my $CPU = 4;
my $output_dir = "DetonateData";
my $species_opts = "mouse|human|fission_yeast";
my $usage = <<__EOUSAGE__;
#######################################################################################
#
# (note, must set env var DETONATE_HOME to installation directory of DETONATE software)
#
# --reads <string> if paired-end, list as comma-delimited: "left.fq,right.fq"
#
# --target <string> target fasta file (eg. Trinity.fasta)
#
# --frag_len <string> frag length. If SE data, it's the read length.
#
# --species <string> $species_opts (param files provided at: rsem-eval/true_transcript_length_distribution/)
#
# optional:
#
# --SS_lib_type <string> R, F, RF, or FR
#
# --threads <int> number of threads to use in multi-threading (default: $CPU)
#
# --output_dir <string> default: $output_dir
#
########################################################################################
__EOUSAGE__
;
my $reads;
my $target;
my $frag_len;
my $SS_lib_type;
my $species;
&GetOptions ( 'h' => \$help_flag,
'reads=s' => \$reads,
'target=s' => \$target,
'frag_len=i' => \$frag_len,
'SS_lib_type=s' => \$SS_lib_type,
'threads=i' => \$CPU,
'output_dir=s' => \$output_dir,
'species=s' => \$species,
);
unless ($reads && $target && $frag_len && $species) {
die $usage;
}
main: {
my $detonate_home_dir = $ENV{DETONATE_HOME} or die "Error, must set env var DETONATE_HOME to its installation directory";
unless (defined($species) && $species =~ /$species_opts/) {
die "Error, species $species not supported, only $species_opts";
}
my $cmd = "$detonate_home_dir/rsem-eval/rsem-eval-calculate-score -p $CPU "
. " --transcript-length-parameters $detonate_home_dir/rsem-eval/true_transcript_length_distribution/$species.txt "
. " $reads $target $output_dir $frag_len ";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
else {
print STDERR "Done.\n";
}
exit(0);
}
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