#!/usr/bin/env perl
use strict;
use warnings;
use Bio::Factory::EMBOSS;
my $usage = "perl $0 in.fq out.fa";
my $infile = shift or die $usage;
my $outfile = shift or die $usage;
my $factory = Bio::Factory::EMBOSS->new;
my $seqret = $factory->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication object
$seqret->run({-sequence => $infile,
-sformat1 => 'fastq',
-outseq => $outfile,
-osformat => 'fasta'});
