--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/spades_3_0/spades.pl	Wed Feb 05 05:19:03 2014 -0500
@@ -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 = 'output_dir';
+# 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 $!;
+    print TAB "#name\tlength\tcoverage\n";
+    while (<FASTA>){
+	next unless /^>/;
+	chomp;
+	die "Not all elements found in $_\n" if (! m/^>NODE_(\d+)_length_(\d+)_cov_(\d+\.*\d*)/);
+	my ($n, $l, $cov) = ($1, $2, $3);
+	print TAB "NODE_$n\t$l\t$cov\n";
+    }
+    close TAB;
+}