Bioperl-guts: Re: repetitive DNA

[Ewan Birney]

Hmmm. I like this idea. Perhaps something like:

  # like the SeqIO system. Does some run time loading
  # of filter modules
  $filter = Bio::Filter->new( -type => 'XNU', -paramters => \%param_hash);

  # filterresults has something like Alessandros array of
  # start,end,sequence
  $filterresults = $filter->filter($seq);

  # segments could be Bio::SeqFeature::Generic objects.
  # this means we could add them to AnnSeq objects and provide
  # automatic GFF/EMBL formatting etc.
  foreach my $seg ( $filterresults->segments ) {
	$start = $seg->start;
	$end = $seg->end;
	$seq = $seg->seq(); # a seq object of the portion
  }

  # alternative use of filter - common enough to put in the
  # module
  #
  # masked_seq is a Bio::Seq with N's/X's put in
  $masked_seq = $filter->mask($seq);

What do you think of this Alessandro? (And any other ideas for other
people?)



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Ewan Birney. Work: +44 (0)1223 494992. Mobile: +44 (0)7970 151230
<birney@sanger.ac.uk>
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