run_DESeq_wrapper.pl

#!/usr/bin/perl

use strict;
use Getopt::Long qw(GetOptions);


my ($config, $bin, $species, $counts, $samplekey, $comparisons, $clusterOnly, $diff_out, $count_out, $cluster_out, $gsa_out, $help, $no_replicates, $Rlibs);

my $pre = 'TEMP';
GetOptions ('pre=s' => \$pre,
	    'config=s' => \$config,
	    'bin=s' => \$bin,
	    'species=s' => \$species,
	    'counts=s' => \$counts,
	    'samplekey=s' => \$samplekey,
	    'comparisons=s' => \$comparisons,
	    'diff_out=s' => \$diff_out,
	    'count_out=s' => \$count_out,
	    'cluster_out=s' => \$cluster_out,
	    'gsa_out=s' => \$gsa_out,
 	    'clusterOnly' => \$clusterOnly,
            'no_replicates' => \$no_replicates,
            'Rlibs=s' => \$Rlibs,
	    'help' => \$help) or exit(1);

my $R = '';
open(CONFIG, "$config") or die "CAN'T OPEN CONFIG FILE $config $!";
while(<CONFIG>){
    chomp;
    
    my @conf = split(/\s+/, $_);
    if($conf[0] =~ /^r$/i){
	if(!-e "$conf[1]/R"){
	    die "CAN'T FIND R IN $conf[1] $!";
	}
	$R = $conf[1];
    }
}
close CONFIG;

`export R_LIBS=$Rlibs:\$R_LIBS`;

my $run_gsa = "gsa.dir='$gsa_out'";
my $gmt_dir = "''";
if(!$gsa_out){ 
    $run_gsa = "GSA=FALSE";
} else {
    if($species =~ /hg19|human/i){
        $gmt_dir = "gmt.dir='$bin/data/human/MSigDB/v7.1'";
    } else {
        if($species =~ /mm9|mm10|mouse/i){
            $gmt_dir = "gmt.dir='$bin/data/mouse/MSigDB/v7.1'";
        }
    }
}


my $ec = 0;

if($clusterOnly){
    print "COMMAND: $R/Rscript $bin/RunDE.R \"bin='$bin'\" \"pre='$pre'\" \"counts.file='$counts'\" \"counts.dir='$count_out'\" \"$run_gsa\" \"clustering.dir='$cluster_out'\" \"Rlibs='$Rlibs'\" \n";
    `$R/Rscript $bin/RunDE.R "bin='$bin'" \"pre='$pre'\" "counts.file='$counts'" "counts.dir='$count_out'" "$run_gsa" "clustering.dir='$cluster_out'" "Rlibs='$Rlibs'"`;
    $ec = $? >> 8;
}
else{
    open(COMP, "$comparisons") || die "Can't open comparisons file $comparisons $!";
    my @comps = ();
    while(<COMP>){
	chomp;
	
	my @com = split(/\s+/, $_);
	push @comps, "'$com[0] - $com[1]'";
    }
    close COMP;
    
    my $cmpStr = join(",", @comps);
    my $reps = "";
    if($no_replicates){
        $reps = "no.replicates=TRUE";
    }

    print "command: $R/Rscript $bin/RunDE.R \"bin='$bin'\" \"$gmt_dir\" \"pre='$pre'\"  \"species='$species'\" \"proj.id='$pre'\" \"diff.exp.dir='$diff_out'\" \"counts.file='$counts'\" \"counts.dir='$count_out'\" \"clustering.dir='$cluster_out'\" \"$run_gsa\" \"key.file='$samplekey'\" \"comps=c($cmpStr)\" \"$reps\" \"pre='$pre'\" \"Rlibs='$Rlibs'\"\n";


    `$R/Rscript $bin/RunDE.R "bin='$bin'" "$gmt_dir" \"pre='$pre'\" "species='$species'" "proj.id='$pre'" "diff.exp.dir='$diff_out'" "counts.file='$counts'" "pre='$pre'" "counts.dir='$count_out'" "clustering.dir='$cluster_out'" "$run_gsa" "key.file='$samplekey'" "comps=c($cmpStr)" "$reps" "Rlibs='$Rlibs'"`;

    $ec = $? >> 8;
}

if($ec != 0){ die "Error(s) caught from RunDE.R"; }