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annotate spades.pl @ 0:addd8265834b draft default tip

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