fastq-to-fasta

#!/usr/bin/perl

use Getopt::Long;

GetOptions(\%opt, "i=s", "o=s", "h");

$ARGV[0]=$opt{i} if $opt{i};
$ARGV[0]="gunzip -c $ARGV[0]|" if $ARGV[0] =~ /\.gz$/;

if ($opt{o}) {
    open (STDOUT, ($opt{o} =~ /\.gz$/ ? "|gzip -c >$opt{o}" : ">$opt{o}")) || die "$opt{o}:$!\n";
}

print(usage()) && exit if $opt{h};

while($i=<>) {
    $s=<>;
    $c=<>;
    $q=<>;
    die "Bad fastq at like $." unless $i =~ s/^@/>/;
    print $i, $s;
}

sub usage {
<<EOF
usage: fastq_to_fasta [-h] [[-i] INFILE] [-o OUTFILE]

   [-h]         = This helpful help screen.
   [-i INFILE]  = FASTA/Q input file. default is STDIN.
   [-o OUTFILE] = FASTA output file. default is STDOUT.

If input, or output, ends in '.gz' then the file is
gunzipped/gzipped.
EOF
}