Mercurial > repos > edward-kirton > roche454_toolsuite

annotate roche454/runMapping_cDNA_wrapper.pl @ 1:368a6ebebdde

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:51:04 -0400
parents f036c7107601
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
1 #!/usr/bin/env/perl
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
2
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
3 use warnings;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
4 use strict;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
5 use File::Copy;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
6
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
7 # EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
8 my $outdir=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
9 my $alignment_info=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
10 my $all_contigs_fasta=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
11 my $all_contigs_qual=shift @ARGV;
1
368a6ebebdde Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
edward-kirton
parents: 0
diff changeset
12 my $all_diffs=shift @ARGV;
368a6ebebdde Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
edward-kirton
parents: 0
diff changeset
13 my $all_struct_vars=shift @ARGV;
368a6ebebdde Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
edward-kirton
parents: 0
diff changeset
14 my $hc_diff=shift @ARGV;
368a6ebebdde Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
edward-kirton
parents: 0
diff changeset
15 my $hc_struct_vars=shift @ARGV;
368a6ebebdde Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
edward-kirton
parents: 0
diff changeset
16 my $mapping_qc=shift @ARGV;
0
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
17 my $newbler_metrics=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
18 my $pair_align=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
19 my $read_status=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
20 my $ref_status=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
21 my $tag_pair_align=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
22 my $trim_status=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
23 my $trimmed_reads_fasta=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
24 my $trimmed_reads_qual=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
25 my $contigs_ace=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
26 my $gene_status=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
27 my $isotigs_ace=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
28 my $isotigs_fasta=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
29 my $isotigs_qual=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
30 my $isotigs_agp=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
31 my $isotigs_layout=shift @ARGV;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
32
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
33 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
34
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
35 my @cmd=removeUnusedOptions(@ARGV);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
36
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
37 # RUN COMMAND
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
38 # NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
39 my $stderr;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
40 eval { $stderr=`@cmd 2>&1`; };
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
41 if ( $@ ) {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
42 print STDERR "Newbler ERROR: $stderr\n";
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
43 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
44 die($@);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
45 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
46
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
47 get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
48 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
49 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
50 get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
51 get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
52 get_outfile("$outdir/454HCDiff.txt", $hc_diff);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
53 get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
54 get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
55 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
56 get_outfile("$outdir/454PairAlign.txt", $pair_align);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
57 get_outfile("$outdir/454ReadStatus.txt", $read_status);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
58 get_outfile("$outdir/454RefStatus.txt", $ref_status);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
59 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
60 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
61 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
62 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
63 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
64 get_outfile("$outdir/454GeneStatus.txt", $gene_status);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
65 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
66 get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
67 get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
68 get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
69 get_outfile("$outdir/454IsotigsLayout.txt", $isotigs_layout);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
70 exit;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
71
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
72 # EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
73 sub removeUnusedOptions {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
74 my @cmd=();
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
75 my $prev;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
76 foreach (@_) {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
77 unless ($_ eq 'None') {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
78 push @cmd, $prev if defined($prev);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
79 $prev=$_;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
80 } else {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
81 $prev=undef;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
82 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
83 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
84 push @cmd, $prev if defined($prev);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
85 return @cmd;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
86 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
87
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
88 sub get_outfile {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
89 my ($src, $dest)=@_;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
90 # make sure dest defined and src exist; skip if dest is 'None'
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
91 if ( $dest and $dest ne 'None' and $src and -f $src ) {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
92 move($src,$dest);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
93 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
94 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
95
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
96 __END__