[Biopython-dev] [Bug 2285] Creating Bio.AlignIO to cope with alignments like Bio.SeqIO does sequences

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed May 2 18:44:01 UTC 2007


------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2007-05-02 14:44 EST -------
Created an attachment (id=643)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=643&action=view)
ZIP file containing four python scripts to go in Bio/AlignIO/*.py

There is a follow up patch to Bio/SeqIO/__init__.py to basically use
Bio.AlignIO for reading/writing clustal, stockholm and phylip instead.  The
corresponding parsers under Bio/SeqIO/*.py would then be removed.

I have not yet worked out what a Nexus file looks like when it holds more than
one alignment (if in fact this is possible).

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