view tools/spades_2_4/spades.pl @ 0:a407a6ed437d draft

Uploaded version 0.2, tested on the toolshed

#!/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;

# Parse arguments
my ($out_contigs_file, $out_scaffolds_file, $out_log_file, @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();
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;
}