Mercurial > repos > edward-kirton > roche454_toolsuite

annotate roche454/runAssembly_cDNA_wrapper.pl @ 0:f036c7107601

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
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 23 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 $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
10 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
11 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
12 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
13 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
14 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
15 my $all_contigs_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
16 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
17 my $contigs_consed_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
18 my $contig_graph=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 $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
20 my $pair_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 $scaffolds_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
22 my $scaffolds_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
23 my $scaffolds_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
24 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
25 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
26 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
27 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
28 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
29 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
30 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
31
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
32 # 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
33
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
34 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
35
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
36 # RUN COMMAND
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
37 # 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
38 my $stderr;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
39 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
40 if ( $@ ) {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
41 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
42 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
43 die($@);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
44 }
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 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
47 get_outfile("$outdir/454ReadStatus.txt", $read_status);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
48 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
49 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
50 get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
51 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
52 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
53 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
54 get_outfile("$outdir/consed/edit_dir/454Contigs.ace.1", $contigs_consed_ace);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
55 get_outfile("$outdir/454ContigGraph.txt", $contig_graph);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
56 get_outfile("$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/454PairStatus.txt", $pair_status);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
58 get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
59 get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
60 get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
61 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
62 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
63 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
64 get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
65 get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
66 get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
67 get_outfile("$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
68 exit;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
69
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
70 # 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
71 sub removeUnusedOptions {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
72 my @cmd=();
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
73 my $prev;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
74 foreach (@_) {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
75 unless ($_ eq 'None') {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
76 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
77 $prev=$_;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
78 } else {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
79 $prev=undef;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
80 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
81 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
82 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
83 return @cmd;
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
84 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
85
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
86 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
87 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
88 # 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
89 if ( $dest and $dest ne 'None' and $src and -f $src ) {
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
90 move($src,$dest);
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
91 }
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
92 }
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 __END__