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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 17:21:54 -0400
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f955d9559654 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
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2
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3 use strict;
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4 use warnings;
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5 use File::Copy;
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6
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7 die("ERROR: Expected at least 8 arguments; got: @ARGV\n") unless @ARGV >= 8;
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8
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9 # GET ARGS
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10 my $kmer_size=shift @ARGV;
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11 my $min_num_pairs=shift @ARGV;
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12 my $outdir=shift @ARGV;
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13 my $outfile=shift @ARGV;
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14 my $contigs_outfile=shift @ARGV;
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15 my $sam_outfile=shift @ARGV;
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16 my $hist_outfile=shift @ARGV;
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17
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18 # ALL FILES GO IN THIS extra_files_path
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19 unless (-d $outdir) {
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20 mkdir $outdir or die("Unable to make dir, $outdir\n");
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21 }
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22 chdir $outdir;
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23
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24 # RUN COMMAND
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25 `abyss-pe k=$kmer_size n=$min_num_pairs in='@ARGV' name=abyss 2> $outdir/abyss.stderr > $outdir/abyss.stdout`;
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26 if ($? != 0) {
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27 unless ( -s "$outdir/abyss-3.hist") { print STDERR "NO CONTIGS WERE PRODUCED!\n" }
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28 open(IN, "<$outdir/abyss.stdout") or die($!);
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29 while (<IN>) { print STDERR $_ }
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30 close IN;
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31 die("ABORTING\n");
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32 }
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33
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34 # FILTER HISTOGRAM
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35 open (IN, "<$outdir/abyss.stderr") or die($!);
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36 open (OUT, ">$outfile") or die($!);
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37 while (my $line=<IN>) {
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38 my @chars=split(//, $line);
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39 my $filter=0;
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40 foreach my $char (@chars) {
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41 if (ord($char) >= 129) {
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42 $filter=1;
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43 last;
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44 }
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45 }
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46 print OUT $line unless $filter;
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47 }
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48 close IN;
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49 close OUT;
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50 unlink("$outdir/abyss.stderr");
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51
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52 # OUTPUT INFO LINE TEXT
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53 open(IN, "<$outdir/abyss.stdout") or die($!);
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54 while (<IN>) {
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55 if (/^Assembled \d+ k\-mer in \d+ contigs/) {
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56 print;
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57 last;
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58 }
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59 }
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60 close IN;
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61
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62 # GALAXY DOESN'T WANT GZIPPED DATAFILES
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63 run("gunzip $outdir/abyss-3.sam.gz");
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64
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65 # MOVE OUTFILES
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66 mv_outfile("$outdir/abyss-contigs.fa", $contigs_outfile);
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67 mv_outfile("$outdir/abyss-3.sam", $sam_outfile);
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68 mv_outfile("$outdir/coverage.hist", $hist_outfile);
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69 exit;
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70
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71 sub run {
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72 my $cmd=shift;
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73 my $output=`$cmd 2>&1`;
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74 if ($? != 0) {
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75 print STDERR "ERROR RUNNING COMMAND: $cmd\n";
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76 die($output);
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77 }
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78 return $output;
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79 }
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80
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81
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82 sub mv_outfile {
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83 my ($src,$dest)=@_;
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84 # if dest defined and src exist, then move outfiles to galaxy-specified location
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85 if ( $dest ne 'None' and -f $src ) {
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86 unlink($dest);
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87 move($src,$dest);
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88 }
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89 }
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90 __END__