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|
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use Cwd;
######################################################
## Set to base directory of the Trinity installation:
my $BASEDIR = "$FindBin::RealBin/../";
######################################################
my $usage = <<__EOUSAGE__;
##########################################################################################################
#
# Required:
#
# --samples_file <string> tab-delimited text file indicating biological replicate relationships.
# ex.
# cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq
# cond_A cond_A_rep2 A_rep2_left.fq A_rep2_right.fq
# cond_B cond_B_rep1 B_rep1_left.fq B_rep1_right.fq
# cond_B cond_B_rep2 B_rep2_left.fq B_rep2_right.fq
#
# # note, include Trinity parameters in the sample file like so:
# --CPU=6
# --max_memory=10G
# --seqType=fq
# --SS_lib_type=RF
#
###########################################################################################################
__EOUSAGE__
;
my $help_flag;
my $read_samples_descr_file;
&GetOptions ( 'h' => \$help_flag,
'samples_file=s' => \$read_samples_descr_file,
);
if ($help_flag || ! $read_samples_descr_file) {
die $usage;
}
my $workdir = cwd();
my @PARAMS;
my %conditions_to_read_info = &parse_sample_descriptions($read_samples_descr_file, \@PARAMS);
my @conditions = sort keys %conditions_to_read_info;
my @left_fq_files;
my @right_fq_files;
foreach my $condition (@conditions) {
my $replicates_href = $conditions_to_read_info{$condition};
my @replicates = keys %$replicates_href;
foreach my $replicate (@replicates) {
my ($left_fq_file, $right_fq_file) = @{$replicates_href->{$replicate}};
if (-s $left_fq_file) {
push (@left_fq_files, $left_fq_file);
}
else {
die "Error, cannot locate file: [$left_fq_file] ";
}
if ($right_fq_file) {
if (-s $right_fq_file) {
push (@right_fq_files, $right_fq_file);
}
else {
die "Error, cannot locate file: [$right_fq_file]";
}
}
}
}
## Run Trinity:
my $cmd = "";
if (@left_fq_files && @right_fq_files) {
$cmd = "$BASEDIR/Trinity --left " . join(",", @left_fq_files) . " --right " . join(",", @right_fq_files);
}
else {
# run left as single
$cmd = "$BASEDIR/Trinity --single " . join(",", @left_fq_files);
}
$cmd .= " " . join(" ", @PARAMS);
print STDERR "CMD: $cmd\n\n";
my $ret = system($cmd);
if ($ret) {
die "Error, CMD: $cmd died with ret: $ret";
}
exit(0);
####
sub parse_sample_descriptions {
my ($read_samples_descr_file, $params_aref) = @_;
my %samples_descr;
open (my $fh, $read_samples_descr_file) or die $!;
while (<$fh>) {
if (/^\#/) { next; }
unless (/\w/) { next; }
s/^\s+|\s+$//g;
chomp;
if (/^\-/) {
## a parameter
push (@$params_aref, $_);
}
else {
my @x = split(/\t/);
my ($condition, $replicate, $reads_left, $reads_right) = @x;
$samples_descr{$condition}->{$replicate} = [$reads_left, $reads_right];
}
}
close $fh;
return(%samples_descr);
}
|
