http://www.perlmonks.org?node_id=847642


in reply to Reading in Qual File Using Bio::SeqIO

This qual format is similar to FastA but it has its own module interfaces at 'Bio::Seq::PrimaryQual' and Bio::SeqIO::qual, you are mixing between Bio::SeqIO and the others since Bio::SeqIO is the general wrapper for many other packages that intelligently handle many different formats each having their own peculiarities. It is still flexibly possible to interchange methods under such a generalized wrapper btw with some significant differences (read 'potential for things to go wrong!')...

However BioPerl can gift you valuable hints were you adhering to and observing the mantra of: 

use strict;
use warnings;

[download]
at the top of your program and declaring your variable accordingly, this can save you needless tail-chasing.

$qual_obj->seq is better written as $qual_obj->qual 
use strict;
use warnings;
use Bio::SeqIO::qual;
my $file = "Qual.txt";

my $qual_obj = Bio::SeqIO::qual->new(-file =>"<$file",-format=>'qual',
+);

my %qual_hash ;
while(my $qual = $qual_obj->_next_qual){
        $qual_hash{$qual->id}= $qual->qual();
        }
use Data::Dumper;
print Dumper(\%qual_hash);

[download]
The above code's $qual_obj can still be initialized directly through Bio::SeqIO: 
use strict;
use warnings;

use Bio::SeqIO;
my $file = "Qual.txt";
my $qual_obj = Bio::SeqIO->new(-file =>"<$file",-format=>'qual',);

[download]

You can also read this file in as a FastA file since it has the '>' record identifier, however, each qual record would not be indexed in an array as is the case in the above example since reading the file as a FastA would slurp in all qual values into a single string that is treated as a protein sequence by BioPerl. 

#THIS DOESN'T READ THE FILE RIGHT..

my $file = "Qual.txt";
my $qual_obj = Bio::SeqIO->new(-file =>"<$file",-format=>'fasta',);

my %seq_hash = ();
while(my $seq= $qual_obj->next_seq){
        $seq_hash{$seq->id} = $seq->seq;
        }

use Data::Dumper;
print Dumper(\%seq_hash);

[download]
Kudos for providing examples of code and input :)...

Excellence is an Endeavor of Persistence. A Year-Old Monk :D .

Replies are listed 'Best First'.
Re^2: Reading in Qual File Using Bio::SeqIO
by twaddlac (Novice) on Jul 02, 2010 at 18:43 UTC
    Thank you very much @biohisham!! Reading in the qual like a fasta works like a charm!! :-)
[reply]
Re^2: Reading in Qual File Using Bio::SeqIO
by twaddlac (Novice) on Jul 06, 2010 at 19:09 UTC

    Well I have unfortunately encountered another error. I read the qual file in like a fastA file and put it into a hash and I can't write it like a qual file for some reason.. is there some sort of parsing that I have to do that the BioPerl modules won't do for me?

    --------------------- WARNING ---------------------
MSG: seq doesn't validate, mismatch is 4040404040404040404040404040404
+040404040404040404040404040404040404040393737373737373737373737373737
+373737373535353535353030302828283030323235373737373737373737373737373
+737373737373737373737373737373535353737343232323232323230161515152427
+2626131313232313131317212121212119211618171918
---------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Attempting to set the sequence to [404040404040404040404040404040
+404040404040404040404040404040404040404039373737373737373737373737373
+737373737353535353535303030282828303032323537373737373737373737373737
+373737373737373737373737373737353535373734323232323232323016151515242
+72626131313232313131317212121212119211618171918] which does not look 
+healthy
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/
+Root.pm:357
STACK: Bio::PrimarySeq::seq /usr/lib/perl5/site_perl/5.8.8/Bio/Primary
+Seq.pm:270
STACK: Bio::PrimarySeq::new /usr/lib/perl5/site_perl/5.8.8/Bio/Primary
+Seq.pm:221
STACK: Bio::Seq::new /usr/lib/perl5/site_perl/5.8.8/Bio/Seq.pm:484
STACK: tagfinder.pl:227

    [download]
[reply]
[d/l]

In Section Seekers of Perl Wisdom