See fastqpl and BioPerl. Please, clarify the question, so we can help. It's not clear what's the question exactly is

I have seen more questions on parsing fastq and I am a little disappointed by the efficiency of the BioPerl and BioPython fastq parsers (see also my answer to this question). In the end, I decided to port my fasta/q parser to Perl/Python. This is readfq. It works for multi-line fastq and is by far faster than bioperl. The following is an example. To use readfq, you only need to copy-and-paste the `readfq()` function. The Perl version has not been commented or optimized.

sub readfq {
    my ($fh, $aux) = @_;
    @$aux = [undef, 0] if (!defined(@$aux));
    return if ($aux->[1]);
    if (!defined($aux->[0])) {
        while (<$fh>) {
            chomp;
            if (substr($_, 0, 1) eq '>' || substr($_, 0, 1) eq '@') {
                $aux->[0] = $_;
                last;
            }
        }
        if (!defined($aux->[0])) {
            $aux->[1] = 1;
            return;
        }
    }
    my $name = /^.(\S+)/? $1 : '';
    my $seq = '';
    my $c;
    $aux->[0] = undef;
    while (<$fh>) {
        chomp;
        $c = substr($_, 0, 1);
        last if ($c eq '>' || $c eq '@' || $c eq '+');
        $seq .= $_;
    }
    $aux->[0] = $_;
    $aux->[1] = 1 if (!defined($aux->[0]));
    return ($name, $seq) if ($c ne '+');
    my $qual = '';
    while (<$fh>) {
        chomp;
        $qual .= $_;
        if (length($qual) >= length($seq)) {
            $aux->[0] = undef;
            return ($name, $seq, $qual);
        }
    }
    $aux->[1] = 1;
    return ($name, $seq);
}

my @aux = undef;
my ($n, $slen, $qlen) = (0, 0, 0);
while (my ($name, $seq, $qual) = readfq(\*STDIN, \@aux)) {
    ++$n;
    $slen += length($seq);
    $qlen += length($qual) if ($qual);
}
print join("\t", $n, $slen, $qlen), "\n";

How about fastq_to_fasta? I think that is exactly what you are asking for (except it's not a perl script).

I had a script close to what you want so I modified it a little bit and I think it now will give what you want; one fastq file for each sequence in the input fastq file.

One drawback of this script is that it expects each sequence to be only 4 lines long (i.e. no wrapping of the sequences). It's highly possible that your files really only contain 4 lines per sequence (as I understand from the sample you copy/pasted in the beginning) but you should check them again to be sure!

#!/bin/perl -w

use strict;

open ( IN, $ARGV[0] ) or die;

my $counter = 0;
while ( my $in_line = <IN> ) {

    # assuming only 4 lines per sequence!
    my $sequence = "";

    # add the sequence header
    $sequence .= $in_line;

    # add the sequence
    $in_line = <IN>;
    $sequence .= $in_line;

    # add the quality header
    $in_line = <IN>;
    $sequence .= $in_line;

    # add the quality
    $in_line = <IN>;
    $sequence .= $in_line;

    open ( OUT, ">sequence.$counter.fastq" ) or die;
    print OUT $sequence;
    close OUT;

    $counter++;
}

I think my asking question was only wrong as nobody is getting what I actually wanted the script to do, sorry for these. I have a look around to other questions over here and almost similar type question was there asked with title - Split Fastq file into different files only comprising one chromosome each.

And answer was - seqretsplit -sformat fastq-sanger -osformat fastq test.fastq

which actually was splitting the sequences

So far I was trying it with Bioperl

#!/bin/perl -w

use Bio::SeqIO;

$in = Bio::SeqIO->new(-file=> "test.fastq", -format =>"fastq"

                          );

$out = Bio::SeqIO->new(-file=>">test", -format =>"fasta");

while ( my $seq = $in->next_seq() ) {$out->write_seq($seq); }

which was giving all sequences in one file not in separate.