diff 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/velvet/velveth_jgi_wrapper.pl	Tue Jun 07 17:52:16 2011 -0400
@@ -0,0 +1,31 @@
+#!/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