annotate velvet/velveth_jgi_wrapper.pl @ 0:4afe13ac23b6 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

#!/usr/bin/env perl

use strict;
use warnings;
my $start=time;
my $outfile=shift @ARGV;
my $outdir=shift @ARGV;
my $kmer=$ARGV[2];
die ("USER ERROR: Hash length (kmer) must be odd!\n") unless $kmer % 2;
my $tot_reads=0;
open (VELVETH, "@ARGV 2>&1|") or die("Unable to run velveth: $!\n");
open(OUT, ">$outfile") or die($!);
while (<VELVETH>) {
    print OUT $_;
    if (/^\[\d+\.\d+\] (\d+) sequences found/) {
        $tot_reads += $1;
    }
}
close VELVETH;
close OUT;
die("No reads found\n") unless $tot_reads;
my $sec=time-$start;
my $min=int($sec/60);
$sec -= ($min*60);
my $hr=int($min/60);
$min -= ($hr*60);
print "$tot_reads processed in";
print " $hr hr" if $hr;
print " $min min" if $min;
print " $sec sec\n";
exit