Mercurial > repos > edward-kirton > velvet_toolsuite
comparison 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
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:52:16 -0400 |
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-1:000000000000 | 0:4afe13ac23b6 |
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1 #!/usr/bin/env perl | |
2 | |
3 use strict; | |
4 use warnings; | |
5 my $start=time; | |
6 my $outfile=shift @ARGV; | |
7 my $outdir=shift @ARGV; | |
8 my $kmer=$ARGV[2]; | |
9 die ("USER ERROR: Hash length (kmer) must be odd!\n") unless $kmer % 2; | |
10 my $tot_reads=0; | |
11 open (VELVETH, "@ARGV 2>&1|") or die("Unable to run velveth: $!\n"); | |
12 open(OUT, ">$outfile") or die($!); | |
13 while (<VELVETH>) { | |
14 print OUT $_; | |
15 if (/^\[\d+\.\d+\] (\d+) sequences found/) { | |
16 $tot_reads += $1; | |
17 } | |
18 } | |
19 close VELVETH; | |
20 close OUT; | |
21 die("No reads found\n") unless $tot_reads; | |
22 my $sec=time-$start; | |
23 my $min=int($sec/60); | |
24 $sec -= ($min*60); | |
25 my $hr=int($min/60); | |
26 $min -= ($hr*60); | |
27 print "$tot_reads processed in"; | |
28 print " $hr hr" if $hr; | |
29 print " $min min" if $min; | |
30 print " $sec sec\n"; | |
31 exit |