Mercurial > repos > edward-kirton > velvet_toolsuite

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:52:16 -0400
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4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #!/usr/bin/env perl
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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2
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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3 use strict;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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4 use warnings;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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5 my $start=time;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 my $outfile=shift @ARGV;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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7 my $outdir=shift @ARGV;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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8 my $kmer=$ARGV[2];
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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9 die ("USER ERROR: Hash length (kmer) must be odd!\n") unless $kmer % 2;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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10 my $tot_reads=0;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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11 open (VELVETH, "@ARGV 2>&1|") or die("Unable to run velveth: $!\n");
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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12 open(OUT, ">$outfile") or die($!);
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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13 while (<VELVETH>) {
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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14 print OUT $_;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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15 if (/^\[\d+\.\d+\] (\d+) sequences found/) {
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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16 $tot_reads += $1;
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17 }
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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18 }
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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19 close VELVETH;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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20 close OUT;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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21 die("No reads found\n") unless $tot_reads;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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22 my $sec=time-$start;
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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23 my $min=int($sec/60);
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24 $sec -= ($min*60);
4afe13ac23b6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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25 my $hr=int($min/60);
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26 $min -= ($hr*60);
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27 print "$tot_reads processed in";
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28 print " $hr hr" if $hr;
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29 print " $min min" if $min;
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30 print " $sec sec\n";
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31 exit