Mercurial > repos > edward-kirton > roche454_toolsuite

comparison roche454/runMapping_cDNA_wrapper.pl @ 0:f036c7107601

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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 17:50:32 -0400
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children 368a6ebebdde
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-1:000000000000 0:f036c7107601
1 #!/usr/bin/env/perl
2
3 use warnings;
4 use strict;
5 use File::Copy;
6
7 # EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
8 my $outdir=shift @ARGV;
9 my $alignment_info=shift @ARGV;
10 my $all_contigs_fasta=shift @ARGV;
11 my $all_contigs_qual=shift @ARGV;
12 my $all_diffs=shift @ARGV
13 my $all_struct_vars=shift @ARGV
14 my $hc_diff=shift @ARGV
15 my $hc_struct_vars=shift @ARGV
16 my $mapping_qc=shift @ARGV
17 my $newbler_metrics=shift @ARGV;
18 my $pair_align=shift @ARGV;
19 my $read_status=shift @ARGV;
20 my $ref_status=shift @ARGV;
21 my $tag_pair_align=shift @ARGV;
22 my $trim_status=shift @ARGV;
23 my $trimmed_reads_fasta=shift @ARGV;
24 my $trimmed_reads_qual=shift @ARGV;
25 my $contigs_ace=shift @ARGV;
26 my $gene_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/454AlignmentInfo.tsv", $alignment_info);
48 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
49 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
50 get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
51 get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
52 get_outfile("$outdir/454HCDiff.txt", $hc_diff);
53 get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
54 get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
55 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
56 get_outfile("$outdir/454PairAlign.txt", $pair_align);
57 get_outfile("$outdir/454ReadStatus.txt", $read_status);
58 get_outfile("$outdir/454RefStatus.txt", $ref_status);
59 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
60 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
61 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
62 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
63 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
64 get_outfile("$outdir/454GeneStatus.txt", $gene_status);
65 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
66 get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
67 get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
68 get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
69 get_outfile("$outdir/454IsotigsLayout.txt", $isotigs_layout);
70 exit;
71
72 # EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
73 sub removeUnusedOptions {
74 my @cmd=();
75 my $prev;
76 foreach (@_) {
77 unless ($_ eq 'None') {
78 push @cmd, $prev if defined($prev);
79 $prev=$_;
80 } else {
81 $prev=undef;
82 }
83 }
84 push @cmd, $prev if defined($prev);
85 return @cmd;
86 }
87
88 sub get_outfile {
89 my ($src, $dest)=@_;
90 # make sure dest defined and src exist; skip if dest is 'None'
91 if ( $dest and $dest ne 'None' and $src and -f $src ) {
92 move($src,$dest);
93 }
94 }
95
96 __END__