Mercurial > repos > lionelguy > spades
diff tools/spades_2_5/spades.pl @ 1:0f8b2da62d7d draft
Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
author | lionelguy |
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date | Mon, 19 Aug 2013 09:06:17 -0400 |
parents | |
children | b5ce24f34dd7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/spades_2_5/spades.pl Mon Aug 19 09:06:17 2013 -0400 @@ -0,0 +1,84 @@ +#!/usr/bin/env perl +## A wrapper script to call spades.py and collect its output +use strict; +use warnings; +use File::Temp qw/ tempfile tempdir /; +use File::Copy; +use Getopt::Long; + +# Parse arguments +my ($out_contigs_file, + $out_contigs_stats, + $out_scaffolds_file, + $out_scaffolds_stats, + $out_log_file, + @sysargs) = @ARGV; + +## GetOptions not compatible with parsing the rest of the arguments in an array. +## Keeping the not-so-nice parse-in-one-go method, without named arguments. +# GetOptions( +# 'contigs-file=s' => \$out_contigs_file, +# 'contigs-stats=s' => \$out_contigs_stats, +# 'scaffolds-file=s' => \$out_scaffolds_file, +# 'scaffolds-stats=s' => \$out_scaffolds_stats, +# 'out_log_file=s' => \$out_log_file, +# ); + +# my @sysargs = @ARGV; + +# Create temporary folder to store files, delete after use +#my $output_dir = tempdir( CLEANUP => 0 ); +my $output_dir = tempdir( CLEANUP => 1 ); +# Link "dat" files as fastq, otherwise spades complains about file format + +# Create log handle +open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n"; + +# Run program +# To do: record time +&runSpades(@sysargs); +&collectOutput(); +&extractCoverageLength($out_contigs_file, $out_contigs_stats); +&extractCoverageLength($out_scaffolds_file, $out_scaffolds_stats); +print $log "Done\n"; +close $log; +exit 0; + +# Run spades +sub runSpades { + my $cmd = join(" ", @_) . " -o $output_dir"; + my $return_code = system($cmd); + if ($return_code) { + print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n"; + die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n"; + } + return 0; +} + +# Collect output +sub collectOutput{ + # To do: check that the files are there + # Collects output + move "$output_dir/contigs.fasta", $out_contigs_file; + move "$output_dir/scaffolds.fasta", $out_scaffolds_file; + open LOG, '<', "$output_dir/spades.log" + or die "Cannot open log file $output_dir/spades.log: $?"; + print $log $_ while (<LOG>); + return 0; +} + +# Extract +sub extractCoverageLength{ + my ($in, $out) = @_; + open FASTA, '<', $in or die $!; + open TAB, '>', $out or die $!; + while (<FASTA>){ + next unless /^>/; + chomp; + my @a = split(/\s/, $_); + my ($NODE, $n, $LENGTH, $l, $COV, $cov) = split(/_/, $a[0]); + die "Not all elements found in $_\n" unless ($n && $l && $cov); + print TAB "$n\t$l\t$cov\n"; + } + close TAB; +}