comparison pyCRAC/pyFastqDuplicateRemover.pl @ 0:19b20927172d draft

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0:19b20927172d

#!/usr/bin/perl -w
use strict;
use Getopt::Long;

my %opt;


GetOptions(\%opt, "f=s", "r=s", "o=s", "out2=s", "version","id=s");

my $cmnd;

if (exists $opt{version}){
	$cmnd = "python /usr/local/bin/pyFastqDuplicateRemover.py --version";
}
else{
	$cmnd = "python /usr/local/bin/pyFastqDuplicateRemover.py -f $opt{f} -o $opt{id}";

	if(defined $opt{r}){
		$cmnd.= " -r $opt{r}";
	}
}

system $cmnd;



if(defined $opt{r}){
	system "mv $opt{id}"."_1.fasta $opt{o}";
	system "mv $opt{id}"."_2.fasta $opt{out2}";
}
else{
	system "mv $opt{id} $opt{o}";
}