[Bioperl-l] Re ad in a Qual File like a Fasta?

Robert Buels rmb32 at cornell.edu
Thu Jul 1 20:18:58 EDT 2010


You probably want to do something like:

use Bio::SeqIO;

my $qual_in = Bio::SeqIO->new(
    -format => 'qual',
    -file => $ARGV[0],
   );

while( my $q = $qual_in->next_seq ) {
    print "qual for ".$q->id." is: ";
    print "$_ " for @{ $q->qual };
    print "\n";
}


twaddlac wrote:
> Hi,
> 
>      I am having a bit of trouble reading in a qual file; I would like to
> input the qual file into a hash but I can't seem to find a method that
> returns the qual sequence. Any ideas? Thank you in advance!




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