Mercurial > repos > edward-kirton > roche454_toolsuite

comparison runAssembly_cDNA_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 23 FILE HANDLES, SOME OF WHICH MAY BE 'None'
8 die("Missing arguments; expected at least 23, got ".scalar(@ARGV)."\n") unless @ARGV >= 23;
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 $isotigs_ace=shift @ARGV;
28 my $isotigs_fasta=shift @ARGV;
29 my $isotigs_qual=shift @ARGV;
30 my $isotigs_agp=shift @ARGV;
31 my $isotigs_layout=shift @ARGV;
32
33 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
34
35 my @cmd=removeUnusedOptions(@ARGV);
36
37 # RUN COMMAND
38 # NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
39 my $stderr;
40 eval { $stderr=`@cmd 2>&1`; };
41 if ( $@ ) {
42 print STDERR "Newbler ERROR: $stderr\n";
43 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
44 die($@);
45 }
46
47 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
48 get_outfile("$outdir/454ReadStatus.txt", $read_status);
49 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
50 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
51 get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
52 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
53 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
54 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
55 get_outfile("$outdir/consed/edit_dir/454Contigs.ace.1", $contigs_consed_ace);
56 get_outfile("$outdir/454ContigGraph.txt", $contig_graph);
57 get_outfile("$outdir/454PairAlign.txt", $pair_align);
58 get_outfile("$outdir/454PairStatus.txt", $pair_status);
59 get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
60 get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
61 get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
62 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
63 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
64 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
65 get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
66 get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
67 get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
68 get_outfile("$outdir/454IsotigsLayout.txt", $isotigs_layout);
69 exit;
70
71 # EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
72 sub removeUnusedOptions {
73 my @cmd=();
74 my $prev;
75 foreach (@_) {
76 unless ($_ eq 'None') {
77 push @cmd, $prev if defined($prev);
78 $prev=$_;
79 } else {
80 $prev=undef;
81 }
82 }
83 push @cmd, $prev if defined($prev);
84 return @cmd;
85 }
86
87 sub get_outfile {
88 my ($src, $dest)=@_;
89 # make sure dest defined and src exist; skip if dest is 'None'
90 if ( $dest and $dest ne 'None' and $src and -f $src ) {
91 move($src,$dest);
92 }
93 }
94
95 __END__