[Biopython-dev] [Bug 3060] Add ungap method to the SeqRecord?

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http://bugzilla.open-bio.org/show_bug.cgi?id=3060





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2010-06-22 09:11 EST -------
(In reply to comment #0)
> My motivating example is to take an ACE file loaded with SeqIO, remove the
> gaps, and output the contigs as FASTQ or QUAL files. This requires the
> per-letter-annotation to be sliced to match the ungapped sequence.
> 
> Likewise any features fully contained within ungapped regions should be
> retained and their co-ordinates shifted. I'm not sure if we should do anything
> about features spanning a gap - the simple option which I have implemented is
> they are lost. This is done via the existing SeqRecord slicing and addition
> code.

I've been trying building SeqFeature objects for the reads in an ACE file,
http://github.com/peterjc/biopython/tree/ace-reads

In this case when I call the SeqRecord ungap method, many of my read features
are lost with the current implementation (because they included gaps). This
also showed the ungap code to be quite slow for features. I'm going to have
another look at this.

Peter


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