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annotate spades.pl @ 0:009c00203195 draft

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planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
author nml
date Mon, 18 Jan 2016 09:53:28 -0500
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0
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1 #!/usr/bin/env perl
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2 ## A wrapper script to call spades.py and collect its output
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3 use strict;
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4 use warnings;
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5 use File::Temp qw/ tempfile tempdir /;
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6 use File::Copy;
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7 use Getopt::Long;
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8
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9 # Parse arguments
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10 my ($out_contigs_file,
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11 $out_contigs_stats,
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12 $out_scaffolds_file,
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13 $out_scaffolds_stats,
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14 $out_log_file,
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15 $new_name,
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16 @sysargs) = @ARGV;
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17
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18
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19 my $output_dir = 'output_dir';
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20
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21 # Create log handle
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22 open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n";
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23
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24 # Run program
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25 runSpades(@sysargs);
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26 collectOutput($new_name);
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27 extractCoverageLength($out_contigs_file, $out_contigs_stats);
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28 extractCoverageLength($out_scaffolds_file, $out_scaffolds_stats);
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29 print $log "Done\n";
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30 close $log;
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31 exit 0;
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32
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33 # Run spades
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34 sub runSpades {
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35 my $cmd = join(" ", @_) . " -o $output_dir";
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36 my $return_code = system($cmd);
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37 if ($return_code) {
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38 print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
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39 die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
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40 }
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41 return 0;
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42 }
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43
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44 # Collect output
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45 sub collectOutput{
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46 my ($new_name) = @_;
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47
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48 # To do: check that the files are there
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49 # Collects output
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50 if ( not -e "$output_dir/contigs.fasta") {
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51 die "Could not find contigs.fasta file\n";
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52 }
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53 if ( not -e "$output_dir/scaffolds.fasta") {
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54 die "Could not find scaffolds.fasta file\n";
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55 }
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56
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57 #if a new name is given for the contigs and scaffolds, change them before moving them
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58 if ( $new_name ne 'NODE') {
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59 renameContigs($new_name);
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60 }
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61 else {
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62 move "$output_dir/contigs.fasta", $out_contigs_file;
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63 move "$output_dir/scaffolds.fasta", $out_scaffolds_file;
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64 }
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65
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66
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67
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68 open LOG, '<', "$output_dir/spades.log"
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69 or die "Cannot open log file $output_dir/spades.log: $?";
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70 print $log $_ while (<LOG>);
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71 return 0;
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72 }
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73
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74 #Change name in contig and scaffolds file
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75 sub renameContigs{
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76 my ($name) = @_;
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77
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78 open my $in, '<',"$output_dir/contigs.fasta" or die $!;
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79 open my $out,'>', $out_contigs_file;
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80
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81 while ( my $line = <$in>) {
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82 #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
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83 #also move the remainder of the length
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84 if ( $line =~ />NODE_(\d+)_(.+)/) {
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85 $line = ">$name" . "_$1 $2\n";
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86 }
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87 print $out $line;
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88 }
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89 close $in;
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90 close $out;
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91
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92
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93 open $in, '<',"$output_dir/scaffolds.fasta" or die $!;
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94 open $out,'>', $out_scaffolds_file;
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95
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96 while ( my $line = <$in>) {
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97 #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
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98 #also move the remainder of the length
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99 if ( $line =~ />NODE_(\d+)_(.+)/) {
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100 $line = ">$name" . "_$1 $2\n";
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101 }
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102 print $out $line;
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103 }
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104 close $in;
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105 close $out;
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106
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107 }
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108
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109
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110 # Extract
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111 sub extractCoverageLength{
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112 my ($in, $out) = @_;
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113 open FASTA, '<', $in or die $!;
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114 open TAB, '>', $out or die $!;
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115 print TAB "#name\tlength\tcoverage\n";
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116 while (<FASTA>){
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117 next unless /^>/;
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118 chomp;
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119 die "Not all elements found in $_\n" if (! m/^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)/);
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120 my ($name,$n, $l, $cov) = ($1,$2, $3, $4);
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121 print TAB "$name" . "_$n\t$l\t$cov\n";
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122 }
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123 close TAB;
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124 }