Mercurial > repos > edward-kirton > roche454_toolsuite

comparison runMapping_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 #!/jgi/tools/bin/perl -w
2
3 use strict;
4 use File::Copy;
5
6 # EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
7 die("Missing arguments; expected at least 21, got ".scalar(@ARGV)."\n") unless @ARGV >= 21;
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 $large_contigs_fasta=shift @ARGV;
27 my $large_contigs_qual=shift @ARGV;
28 my $gene_status=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/454AlignmentInfo.tsv", $alignment_info);
45 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
46 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
47 get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
48 get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
49 get_outfile("$outdir/454HCDiff.txt", $hc_diff);
50 get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
51 get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
52 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
53 get_outfile("$outdir/454PairAlign.txt", $pair_align);
54 get_outfile("$outdir/454ReadStatus.txt", $read_status);
55 get_outfile("$outdir/454RefStatus.txt", $ref_status);
56 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
57 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
58 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
59 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
60 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
61 get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
62 get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual);
63 get_outfile("$outdir/454GeneStatus.txt", $gene_status);
64 exit;
65
66 # EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
67 sub removeUnusedOptions {
68 my @cmd=();
69 my $prev;
70 foreach (@_) {
71 unless ($_ eq 'None') {
72 push @cmd, $prev if defined($prev);
73 $prev=$_;
74 } else {
75 $prev=undef;
76 }
77 }
78 push @cmd, $prev if defined($prev);
79 return @cmd;
80 }
81
82 sub get_outfile {
83 my ($src, $dest)=@_;
84 # make sure dest defined and src exist; skip if dest is 'None'
85 if ( $dest and $dest ne 'None' and $src and -f $src ) {
86 move($src,$dest);
87 }
88 }
89
90 __END__