Mercurial > repos > cstrittmatter > test_galtrakr_eurl_vtec_wgs_pt_23
diff scripts/spades.pl @ 0:e37910d2c794 draft
planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author | cstrittmatter |
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date | Mon, 20 Jan 2020 15:11:03 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/spades.pl Mon Jan 20 15:11:03 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; +}