[Biopython-dev] [Bug 2535] Support for PIR / NBRF format in Bio.SeqIO

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2535





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-02 13:37 EST -------
My patch doesn't accept the "N1" sequence type mentioned in Bio/NBRF/ValSeq.py

Also when recording a SeqRecord from a non-PIR input, we could try and guess
the sequence type.  The alphabet itself is one clue.  GenBank and EMBL files
should also record if the sequence is linear or circular, as well as a sequence
type.  

For proteins, I don't see how to decide between P1 and F1 though (complete
protein vs protein fragment).  Maybe default to F1?


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