bin/fastq2fasta

#!/usr/bin/env perl

use strict;
use warnings;

use Data::Dumper;
use Getopt::Long;


my $verbose      = 0    ;
my $in_file      = ''   ;
my $fasta_file   = ''   ;
my $quality_file = ''   ;
my $dir          = "./" ;

if ( (@ARGV > 0) && ($ARGV[0] =~ /-h/) ) { &usage(); }
if ( ! GetOptions( 
	   "verbose!"      => \$verbose,
	   "fastq=s"       => \$in_file,
	   "fasta=s"       => \$fasta_file,
	   "quality=s"     => \$quality_file ,
	   "destination=s" => \$dir ,
     ) )
  { print &usage("Missing option"); }

unless ($in_file && (-s $in_file)) {
  &usage("No file $in_file.\n");
}

my $file_eol = "\n" ;

if (-f $in_file){
    $fasta_file = $in_file.".fasta" unless ($fasta_file) ;
    extract_fasta_from_fastq($in_file, $fasta_file , $dir, $file_eol)
}
else{
    print STDERR "No input file $in_file!\n";
}


sub extract_fasta_from_fastq {
   my($fastq, $fasta, $dir, $file_eol) = @_;

   # call fq2fa which will do the extraction. 
   # this code is from fq_all2std.pl from the Maq package and has been modified to 
   # deal with unusual end-of-line characters

   # If necessary, we can pull this and call the Maq script directly

   return &fq2fa($fastq, $fasta, $dir, $file_eol);
}

sub fq2fa {
   my($fastq, $fasta, $dir, $file_eol) = @_;
   # modified code from fq_all2std.pl from Maq package

   my $old_eol = $/;
   $/ = $file_eol;

   open(FASTQ, "<$fastq") or die "could not open fastq file '$fastq': $!";
   open(FASTA, ">$dir/$fasta") or die "could not open fasta file '$dir/$fasta': $!";

   my $line;

   while ( defined($line = <FASTQ>) ) 
   {

       chomp $line;
       
       if ( $line =~ /^@(\S+)/ ) 
       {
           print FASTA ">$1\n";
           $line = <FASTQ>;
           chomp $line;
           print FASTA "$line\n";
           <FASTQ>; 
           <FASTQ>;
       }
   }

   close(FASTA) or die "could not close fasta file '$dir/$fasta': $!";
   close(FASTQ) or die "could not close fastq file '$dir/$fastq': $!";

   $/ = $old_eol;

   return 1;
}


sub usage{
    my ($msg) = @_ ;
    print STDERR "Error: " , ( $msg || -1 ) , "\n";
    exit;
}