fa2fastq

fa2fastq.pl

#!/usr/bin/perl -w
# perl fa2fastq.pl input.fa > output.fastq 
# Contact: Shicheng Guo
# Version 1.3
# Update: 2019-09-08
use strict;

die USAGE() if scalar(@ARGV)<1;
my $file = $ARGV[0];
open FILE, $file;

my ($header, $sequence, $sequence_length, $sequence_quality);
while(<FILE>) {
        chomp $_;
        if ($_ =~ /^>(.+)/) {
                if($header ne "") {
                        print "\@".$header."\n";
                        print $sequence."\n";
                        print "+"."\n";
                        print $sequence_quality."\n";
                }
                $header = $1;
		$sequence = "";
		$sequence_length = "";
		$sequence_quality = "";
        }
	else { 
		$sequence .= $_;
		$sequence_length = length($_); 
		for(my $i=0; $i<$sequence_length; $i++) {$sequence_quality .= "I"} 
	}
}
close FILE;
print "\@".$header."\n";
print $sequence."\n";
print "+"."\n";
print $sequence_quality."\n";

sub USAGE{
        print "\nUSAGE: perl $0 input.fa > output.fastq\n\n";
}