[Bioperl-guts-l] [Bug 2981] Bio::Seq::Quality->trunc() doesn't trim raw_quality in Bio::SeqIO::fastq

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Aug 3 12:29:42 EDT 2010


------- Comment #3 from cjfields at bioperl.org  2010-08-03 12:29 EST -------
I think you are confusing a few things here.  The Bio::Seq::Quality class only
holds PHRED calls and doesn't actually store the -raw_quality string
information (that is only used in the raw data parse, via next_dataset()). 
There is no truncation at the parser level, but one could easily do this via an
intermediate layer:

while (my $data = $in->next_dataset) {
   my $trimmed_data = trim_data($data);
   my $trimmed_seq = Bio::Seq::Quality->new(%$trimmed_data);
   # do stuff with it here

We could probably add a trim callback if that suits your needs.

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