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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 @sysargs) = @ARGV;
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16
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17 ## GetOptions not compatible with parsing the rest of the arguments in an array.
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18 ## Keeping the not-so-nice parse-in-one-go method, without named arguments.
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19 # GetOptions(
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20 # 'contigs-file=s' => \$out_contigs_file,
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21 # 'contigs-stats=s' => \$out_contigs_stats,
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22 # 'scaffolds-file=s' => \$out_scaffolds_file,
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23 # 'scaffolds-stats=s' => \$out_scaffolds_stats,
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24 # 'out_log_file=s' => \$out_log_file,
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25 # );
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26
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27 # my @sysargs = @ARGV;
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28
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29 # Create temporary folder to store files, delete after use
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30 #my $output_dir = tempdir( CLEANUP => 0 );
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31 my $output_dir = 'output_dir';
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32 # Link "dat" files as fastq, otherwise spades complains about file format
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33
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34 # Create log handle
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35 open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n";
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36
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37 # Run program
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38 # To do: record time
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39 &runSpades(@sysargs);
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40 &collectOutput();
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41 &extractCoverageLength($out_contigs_file, $out_contigs_stats);
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42 &extractCoverageLength($out_scaffolds_file, $out_scaffolds_stats);
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43 print $log "Done\n";
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44 close $log;
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45 exit 0;
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46
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47 # Run spades
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48 sub runSpades {
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49 my $cmd = join(" ", @_) . " -o $output_dir";
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50 my $return_code = system($cmd);
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51 if ($return_code) {
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52 print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
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53 die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
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54 }
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55 return 0;
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56 }
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57
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58 # Collect output
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59 sub collectOutput{
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60 # To do: check that the files are there
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61 # Collects output
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62 move "$output_dir/contigs.fasta", $out_contigs_file;
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63 move "$output_dir/scaffolds.fasta", $out_scaffolds_file;
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64 open LOG, '<', "$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 $_ while (<LOG>);
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67 return 0;
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68 }
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69
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70 # Extract
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71 sub extractCoverageLength{
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72 my ($in, $out) = @_;
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73 open FASTA, '<', $in or die $!;
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74 open TAB, '>', $out or die $!;
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75 print TAB "#name\tlength\tcoverage\n";
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76 while (<FASTA>){
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77 next unless /^>/;
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78 chomp;
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79 die "Not all elements found in $_\n" if (! m/^>NODE_(\d+)_length_(\d+)_cov_(\d+\.*\d*)/);
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80 my ($n, $l, $cov) = ($1, $2, $3);
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81 print TAB "NODE_$n\t$l\t$cov\n";
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82 }
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83 close TAB;
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84 }
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