#!/usr/bin/env perl use strict; use File::Basename qw(basename); use Getopt::Long; binmode STDOUT; my ($in, $threads, $wrapper_only); GetOptions( 'in=s' => \$in, 'threads=i' => \$threads, 'wrapper-only' => \$wrapper_only, ) or die "Can't parse command line arguments\n"; if (!defined $in) { die "Input file is not specified\n"; } if (!-e $in or !-f $in) { die "Can't find the input file\n"; } if (!defined $threads) { die "Number of threads is not specified\n"; } my $name = basename($in); $name =~ s/\s/_/g; my $temp_dir = $ENV{'TMPDIR'}; if (!defined $temp_dir) { die "Environment variable 'TMPDIR' is not set\n"; } if (!-e $temp_dir or !-d $temp_dir) { die "Can't find temporary directory\n"; } my $len = `head -n 1 '$in.line-length'`; if ($wrapper_only) { run("fastq-to-fasta <'$in' | fasta-change-line-length --line-length $len"); } else { run("gtz -d '$in' -p $threads -c 2>/dev/null" . " | fastq-to-fasta | fasta-change-line-length --line-length $len"); } sub run { my ($cmd) = @_; my $error = system($cmd); if ($error) { die "Command failed:\n$cmd\n"; } }