#!/usr/bin/env perl use strict; use File::Basename qw(basename); use File::Copy qw(move); use Getopt::Long; my ($out, $level, $threads, $wrapper_only); GetOptions( 'out=s' => \$out, 'level=i' => \$level, 'threads=i' => \$threads, 'wrapper-only' => \$wrapper_only, ) or die "Can't parse command line arguments\n"; if (!defined $out) { die "Output file is not specified\n"; } if (!defined $level) { die "Level is not specified\n"; } if (!defined $threads) { die "Number of threads is not specified\n"; } my $name = basename($out); $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 $temp_prefix = "$temp_dir/$name.gtz-c"; my $temp_fasta = "$temp_prefix-fa"; my $temp_fastq = "$temp_prefix-fq"; my $buf_size = 1000000; my $buffer; binmode STDIN; open(my $FA, '>', $temp_fasta) or die "Can't create temporary file \"$temp_fasta\"\n"; binmode $FA; while (read(STDIN, $buffer, $buf_size)) { print $FA $buffer; } close $FA; run("fasta-guess-line-length.pl '$temp_fasta' >'$out.line-length'"); run("fasta-to-fastq --quality 'A' <'$temp_fasta' >'$temp_fastq'"); if ($wrapper_only) { move($temp_fastq, $out); } else { run("gtz '$temp_fastq' -p $threads -l $level -o '$out.gtz' >/dev/null 2>&1"); rename "$out.gtz", $out; unlink $temp_fastq; } unlink $temp_fasta; sub run { my ($cmd) = @_; my $error = system($cmd); if ($error) { die "Command failed:\n$cmd\n"; } }