[Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Mar 10 20:38:07 UTC 2007


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
             Status|NEW                         |ASSIGNED

------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2007-03-10 15:38 EST -------
I'm having trouble with bugzilla not accepting the attachment, which is a
replacement for Bio/SeqIO/NexusIO.py

This seems to work on my limited testing.  However, the only "validation" I
have done to date is checking that Bio.Nexus can read the alignments I create.

Also, if the input records all have simple "generic" alphabets, the code cannot
decide if they are protein, dna or rna - and raises a ValueError.

Its not fool proof, but it might be better to look at the letters in the actual
sequence at that point and "guess".

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