Mercurial > repos > nml > rnaspades

comparison spades.pl @ 0:addd8265834b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
author nml
date Tue, 09 Aug 2016 10:52:40 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:addd8265834b
1 #!/usr/bin/env perl
2 ## A wrapper script to call spades.py and collect its output
3 use strict;
4 use warnings;
5 use File::Temp qw/ tempfile tempdir /;
6 use File::Copy;
7 use Getopt::Long;
8
9 # Parse arguments
10 my ($out_contigs_file,
11 $out_paths_file,
12 $out_log_file,
13 $new_name,
14 @sysargs) = @ARGV;
15
16
17 my $output_dir = 'output_dir';
18
19 # Create log handle
20 open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n";
21
22 # Run program
23 runSpades(@sysargs);
24 collectOutput($new_name);
25 print $log "Done\n";
26 close $log;
27 exit 0;
28
29 # Run spades
30 sub runSpades {
31 my $cmd = join(" ", @_) . " -o $output_dir";
32 my $return_code = system($cmd);
33 if ($return_code) {
34 print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
35 die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
36 }
37 return 0;
38 }
39
40 # Collect output
41 sub collectOutput{
42 my ($new_name) = @_;
43
44 # To do: check that the files are there
45 # Collects output
46 if ( not -e "$output_dir/transcripts.fasta") {
47 die "Could not find transcripts.fasta file\n";
48 }
49 if ( not -e "$output_dir/transcripts.paths") {
50 die "Could not find transcripts.paths file\n";
51 }
52
53 #if a new name is given for the contigs, change them before moving them
54 if ( $new_name ne 'NODE') {
55 renameContigs($new_name);
56 }
57 else {
58 move "$output_dir/transcripts.fasta", $out_contigs_file;
59 move "$output_dir/transcripts.paths", $out_paths_file;
60 }
61
62
63
64 open LOG, '<', "$output_dir/spades.log"
65 or die "Cannot open log file $output_dir/spades.log: $?";
66 print $log $_ while (<LOG>);
67 return 0;
68 }
69
70 #Change name in contig and fastg file
71 sub renameContigs{
72 my ($name) = @_;
73
74 open my $in, '<',"$output_dir/transcripts.fasta" or die $!;
75 open my $out,'>', $out_contigs_file;
76
77 while ( my $line = <$in>) {
78 #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
79 #also move the remainder of the length
80 if ( $line =~ />NODE_(\d+)_(.+)/) {
81 $line = ">$name" . "_$1 $2\n";
82 }
83 print $out $line;
84 }
85 close $in;
86 close $out;
87
88
89 open $in, '<',"$output_dir/transcripts.paths" or die $!;
90 open $out,'>', $out_paths_file;
91
92 while ( my $line = <$in>) {
93 #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
94 #also move the remainder of the length
95 if ( $line =~ />NODE_(\d+)_(.+)/) {
96 $line = ">$name" . "_$1 $2\n";
97 }
98 print $out $line;
99 }
100 close $in;
101 close $out;
102
103 }