fastq and hash table

[manore]

Hello,

I would like to parse the file fastq in order to obtain a hash table with the key ID and value for the next 3 lines.

I use the Bio::SeqIO::fastq module but how to obtain the score line?

my $seqio  = Bio::SeqIO::fastq->new('-format'=>'fastq' , '-file'=>'test.fastq');
while((my $rec = $seqio->next_seq())) {
	my $name = $rec->id();
	my $seq= $rec->seq ;
}

--input--
@HCDPQ1D0501
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT.
+HCDPQ1D0501
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65.....

[kmcarr]

The when reading a fastq file Bio::SeqIO returns a Bio::Seq::Quality object. You can get an array reference to the quality values with the 'qual' method. To display the quality you would dereference the array and then format the list as a string. Here's my version of this:

#!/usr/bin/perl

use strict;
use warnings;

use Bio::SeqIO;

my $inputFile = shift;
my $in = Bio::SeqIO->new(-format=>'fastq', -file=>"$inputFile");

while ( my $data = $in->next_seq() ) {
	my $id = $data->id();
	my $seq = $data->seq();
	my $qualref =  $data->qual();
	my $format = "%2d" . ("%3d" x (@$qualref-1)) . "\n";
	print "$id\n$seq\n";
	printf $format, @$qualref;
}

$qualref is the array reference, dereference using @$qualref and print formatted (printf) output.

[A note about your code above. You should not call Bio::SeqIO::fastq explicitly, just call Bio::SeqIO. The "-format=>'fastq'" parameter then calls the correct module.]