Mercurial > repos > msjeon > abyss_tool

comparison abyss_toolsuite-92636934a189/abyss/abyss-pe_wrapper.pl @ 0:ce99b6666d1f draft

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author msjeon
date Mon, 11 Jun 2012 14:48:15 -0400
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1 #!/usr/bin/env perl
2
3 use strict;
4 use warnings;
5 use File::Copy;
6
7 die("ERROR: Expected at least 8 arguments; got: @ARGV\n") unless @ARGV >= 8;
8
9 # GET ARGS
10 my $kmer_size=shift @ARGV;
11 my $min_num_pairs=shift @ARGV;
12 my $outdir=shift @ARGV;
13 my $outfile=shift @ARGV;
14 my $contigs_outfile=shift @ARGV;
15 my $sam_outfile=shift @ARGV;
16 my $hist_outfile=shift @ARGV;
17
18 # ALL FILES GO IN THIS extra_files_path
19 unless (-d $outdir) {
20 mkdir $outdir or die("Unable to make dir, $outdir\n");
21 }
22 chdir $outdir;
23
24 # RUN COMMAND
25 `abyss-pe k=$kmer_size n=$min_num_pairs in='@ARGV' name=abyss 2> $outdir/abyss.stderr > $outdir/abyss.stdout`;
26 if ($? != 0) {
27 unless ( -s "$outdir/abyss-3.hist") { print STDERR "NO CONTIGS WERE PRODUCED!\n" }
28 open(IN, "<$outdir/abyss.stdout") or die($!);
29 while (<IN>) { print STDERR $_ }
30 close IN;
31 die("ABORTING\n");
32 }
33
34 # FILTER HISTOGRAM
35 open (IN, "<$outdir/abyss.stderr") or die($!);
36 open (OUT, ">$outfile") or die($!);
37 while (my $line=<IN>) {
38 my @chars=split(//, $line);
39 my $filter=0;
40 foreach my $char (@chars) {
41 if (ord($char) >= 129) {
42 $filter=1;
43 last;
44 }
45 }
46 print OUT $line unless $filter;
47 }
48 close IN;
49 close OUT;
50 unlink("$outdir/abyss.stderr");
51
52 # OUTPUT INFO LINE TEXT
53 open(IN, "<$outdir/abyss.stdout") or die($!);
54 while (<IN>) {
55 if (/^Assembled \d+ k\-mer in \d+ contigs/) {
56 print;
57 last;
58 }
59 }
60 close IN;
61
62 # GALAXY DOESN'T WANT GZIPPED DATAFILES
63 run("gunzip $outdir/abyss-3.sam.gz");
64
65 # MOVE OUTFILES
66 mv_outfile("$outdir/abyss-contigs.fa", $contigs_outfile);
67 mv_outfile("$outdir/abyss-3.sam", $sam_outfile);
68 mv_outfile("$outdir/coverage.hist", $hist_outfile);
69 exit;
70
71 sub run {
72 my $cmd=shift;
73 my $output=`$cmd 2>&1`;
74 if ($? != 0) {
75 print STDERR "ERROR RUNNING COMMAND: $cmd\n";
76 die($output);
77 }
78 return $output;
79 }
80
81
82 sub mv_outfile {
83 my ($src,$dest)=@_;
84 # if dest defined and src exist, then move outfiles to galaxy-specified location
85 if ( $dest ne 'None' and -f $src ) {
86 unlink($dest);
87 move($src,$dest);
88 }
89 }
90 __END__