Mercurial > repos > edward-kirton > roche454_toolsuite

comparison runAssembly_wrapper.pl @ 2:2d86d5b112e8

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author edward-kirton
date Thu, 14 Jul 2011 22:14:07 -0400
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children bf1f8bc4abe6
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1:368a6ebebdde 2:2d86d5b112e8
1 #!/usr/bin/env perl
2
3 use warnings;
4 use strict;
5 use File::Copy;
6
7 # EXPECT 20 FILE HANDLES, SOME OF WHICH MAY BE 'None'
8 die("Missing arguments; expected at least 20, got ".scalar(@ARGV)."\n") unless @ARGV >= 20;
9 my $outdir=shift @ARGV;
10 my $newbler_metrics=shift @ARGV;
11 my $read_status=shift @ARGV;
12 my $trimmed_reads_fasta=shift @ARGV;
13 my $trimmed_reads_qual=shift @ARGV;
14 my $alignment_info=shift @ARGV;
15 my $all_contigs_fasta=shift @ARGV;
16 my $all_contigs_qual=shift @ARGV;
17 my $contigs_ace=shift @ARGV;
18 my $contigs_consed_ace=shift @ARGV;
19 my $contig_graph=shift @ARGV;
20 my $pair_align=shift @ARGV;
21 my $pair_status=shift @ARGV;
22 my $scaffolds_fasta=shift @ARGV;
23 my $scaffolds_qual=shift @ARGV;
24 my $scaffolds_agp=shift @ARGV;
25 my $tag_pair_align=shift @ARGV;
26 my $trim_status=shift @ARGV;
27 my $large_contigs_fasta=shift @ARGV;
28 my $large_contigs_qual=shift @ARGV;
29
30 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
31
32 my @cmd=removeUnusedOptions(@ARGV);
33
34 # RUN COMMAND
35 # NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
36 my $stderr;
37 eval { $stderr=`@cmd 2>&1`; };
38 if ( $@ ) {
39 print STDERR "Newbler ERROR: $stderr\n";
40 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
41 die($@);
42 }
43
44 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
45 get_outfile("$outdir/454ReadStatus.txt", $read_status);
46 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
47 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
48 get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
49 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
50 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
51 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
52 get_outfile("$outdir/consed/edit_dir/454Contigs.ace.1", $contigs_consed_ace);
53 get_outfile("$outdir/454ContigGraph.txt", $contig_graph);
54 get_outfile("$outdir/454PairAlign.txt", $pair_align);
55 get_outfile("$outdir/454PairStatus.txt", $pair_status);
56 get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
57 get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
58 get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
59 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
60 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
61 get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
62 get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual);
63 exit;
64
65 # EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
66 sub removeUnusedOptions {
67 my @cmd=();
68 my $prev;
69 foreach (@_) {
70 unless ($_ eq 'None') {
71 push @cmd, $prev if defined($prev);
72 $prev=$_;
73 } else {
74 $prev=undef;
75 }
76 }
77 push @cmd, $prev if defined($prev);
78 return @cmd;
79 }
80
81 sub get_outfile {
82 my ($src, $dest)=@_;
83 # make sure dest defined and src exist; skip if dest is 'None'
84 if ( $dest and $dest ne 'None' and $src and -f $src ) {
85 move($src,$dest);
86 }
87 }
88
89 __END__