--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/spades.pl	Wed Jan 22 08:41:44 2020 -0500
@@ -0,0 +1,133 @@
+#!/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,
+    $new_name,
+    @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: $?\n";
+
+# Run program
+# To do: record time
+runSpades(@sysargs);
+collectOutput($new_name);
+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: $?\n";
+    }
+    return 0;
+}
+
+# Collect output
+sub collectOutput{
+    my ($new_name) = @_;
+    
+    # Collects output
+    #if a new name is given for the contigs and scaffolds, change them before moving them
+    if ( $new_name ne 'NODE') {
+        renameContigs($new_name);
+    }
+    else {
+        if ( -e "$output_dir/contigs.fasta") {
+            move "$output_dir/contigs.fasta", $out_contigs_file;
+        }
+        if ( -e "$output_dir/scaffolds.fasta") {
+            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 $_ while (<LOG>);
+    return 0;
+}
+
+#Change name in contig and scaffolds file
+sub renameContigs{
+    my ($name) = @_;
+
+    open my $in, '<',"$output_dir/contigs.fasta" or die $!;
+    open my $out,'>', $out_contigs_file;
+
+    while ( my $line = <$in>) {
+        #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
+        #also move the remainder of the length
+        if ( $line =~ />NODE_(\d+)_(.+)/) {
+            $line = ">$name" . "_$1 $2\n";
+        }
+        print $out $line;
+    }
+    close $in;
+    close $out;
+    
+
+    open $in, '<',"$output_dir/scaffolds.fasta" or die $!;
+    open $out,'>', $out_scaffolds_file;
+
+    while ( my $line = <$in>) {
+        #remove the NODE_ so we can rebuilt the display_id with our contig name with the contig number.
+        #also move the remainder of the length
+        if ( $line =~ />NODE_(\d+)_(.+)/) {
+            $line = ">$name" . "_$1 $2\n";
+        }
+        print $out $line;
+    }
+    close $in;
+    close $out;
+
+}
+
+
+# Extract
+sub extractCoverageLength{
+    my ($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 $_\n" if (! m/^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)/);
+	my ($name,$n, $l, $cov) = ($1,$2, $3, $4);
+	print TAB "$name" . "_$n\t$l\t$cov\n";
+    }
+    close TAB;
+}