[Bioperl-l] BioPerl and quality files

Chris Fields cjfields at uiuc.edu
Thu Jun 29 11:21:21 EDT 2006


It should work that way, yes:  

my $in = Bio::SeqIO->new(-file => $qual_file , -format => 'qual');

# the below should return a Bio::Seq::Quality object
my $seq = $in->next_seq; 

You might want to check the other SeqIO modules as well depending on your
format:

...

Instances: 2    Module : Bio::SeqIO::abi
Instances: 2    Module : Bio::SeqIO::ctf
Instances: 2    Module : Bio::SeqIO::exp
Instances: 10   Module : Bio::SeqIO::fastq
Instances: 5    Module : Bio::SeqIO::phd
Instances: 3    Module : Bio::SeqIO::raw
Instances: 13   Module : Bio::SeqIO::scf
Instances: 2    Module : Bio::SeqIO::ztr

...

Chris

> Thanks Chris,
> 
> I don't know how I didn't come up with this before. Can I use
> Bio::SeqIO::qual as follows?
> 
> my $in = Bio::SeqIO->new(-file => $qual_file , -format => 'qual');
> 
> Cheers, Wayne
...




More information about the Bioperl-l mailing list