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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Apr 21 12:07:51 EDT 2010


           Summary: Add ungap method to the SeqRecord?
           Product: Biopython
           Version: 1.54b
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk

Biopython 1.53 added an ungap method to the Seq object.

This is a possible enhancement request to add a matching ungap method to the
SeqRecord object, where the per-letter-annotation and features should be
adjusted to match.

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

Patch to follow...

See also Bug 3054 for adding upper and lower methods to the SeqRecord, and the
broader discussion on Bug 2351 about strings, Seq and SeqRecord objects.

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