Mercurial > repos > lionelguy > spades

comparison tools/spades_3_5_0/spades.pl @ 12:85c6121d92a5 draft

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author takadonet
date Tue, 16 Dec 2014 12:57:49 -0500
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11:1027f26f52d5 12:85c6121d92a5
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_contigs_stats,
12 $out_scaffolds_file,
13 $out_scaffolds_stats,
14 $out_log_file,
15 $new_name,
16 @sysargs) = @ARGV;
17
18 ## GetOptions not compatible with parsing the rest of the arguments in an array.
19 ## Keeping the not-so-nice parse-in-one-go method, without named arguments.
20 # GetOptions(
21 # 'contigs-file=s' => \$out_contigs_file,
22 # 'contigs-stats=s' => \$out_contigs_stats,
23 # 'scaffolds-file=s' => \$out_scaffolds_file,
24 # 'scaffolds-stats=s' => \$out_scaffolds_stats,
25 # 'out_log_file=s' => \$out_log_file,
26 # );
27
28 # my @sysargs = @ARGV;
29
30 # Create temporary folder to store files, delete after use
31 #my $output_dir = tempdir( CLEANUP => 0 );
32 my $output_dir = 'output_dir';
33 # Link "dat" files as fastq, otherwise spades complains about file format
34
35 # Create log handle
36 open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n";
37
38 # Run program
39 # To do: record time
40 runSpades(@sysargs);
41 collectOutput($new_name);
42 extractCoverageLength($out_contigs_file, $out_contigs_stats);
43 extractCoverageLength($out_scaffolds_file, $out_scaffolds_stats);
44 print $log "Done\n";
45 close $log;
46 exit 0;
47
48 # Run spades
49 sub runSpades {
50 my $cmd = join(" ", @_) . " -o $output_dir";
51 my $return_code = system($cmd);
52 if ($return_code) {
53 print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
54 die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
55 }
56 return 0;
57 }
58
59 # Collect output
60 sub collectOutput{
61 my ($new_name) = @_;
62
63 # To do: check that the files are there
64 # Collects output
65 if ( not -e "$output_dir/contigs.fasta") {
66 die "Could not find contigs.fasta file\n";
67 }
68 if ( not -e "$output_dir/scaffolds.fasta") {
69 die "Could not find scaffolds.fasta file\n";
70 }
71
72 #if a new name is given for the contigs and scaffolds, change them before moving them
73 if ( $new_name ne 'NODE') {
74 renameContigs($new_name);
75 }
76 else {
77 move "$output_dir/contigs.fasta", $out_contigs_file;
78 move "$output_dir/scaffolds.fasta", $out_scaffolds_file;
79 }
80
81
82
83 open LOG, '<', "$output_dir/spades.log"
84 or die "Cannot open log file $output_dir/spades.log: $?";
85 print $log $_ while (<LOG>);
86 return 0;
87 }
88
89 #Change name in contig and scaffolds file
90 sub renameContigs{
91 my ($name) = @_;
92
93 open my $in, '<',"$output_dir/contigs.fasta" or die $!;
94 open my $out,'>', $out_contigs_file;
95
96 while ( my $line = <$in>) {
97 #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
98 #also move the remainder of the length
99 if ( $line =~ />NODE_(\d+)_(.+)/) {
100 $line = ">$name" . "_$1 $2\n";
101 }
102 print $out $line;
103 }
104 close $in;
105 close $out;
106
107
108 open $in, '<',"$output_dir/scaffolds.fasta" or die $!;
109 open $out,'>', $out_scaffolds_file;
110
111 while ( my $line = <$in>) {
112 #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
113 #also move the remainder of the length
114 if ( $line =~ />NODE_(\d+)_(.+)/) {
115 $line = ">$name" . "_$1 $2\n";
116 }
117 print $out $line;
118 }
119 close $in;
120 close $out;
121
122 }
123
124
125 # Extract
126 sub extractCoverageLength{
127 my ($in, $out) = @_;
128 open FASTA, '<', $in or die $!;
129 open TAB, '>', $out or die $!;
130 print TAB "#name\tlength\tcoverage\n";
131 while (<FASTA>){
132 next unless /^>/;
133 chomp;
134 die "Not all elements found in $_\n" if (! m/^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)/);
135 my ($name,$n, $l, $cov) = ($1,$2, $3, $4);
136 print TAB "$name" . "_$n\t$l\t$cov\n";
137 }
138 close TAB;
139 }