[Biopython-dev] [Bug 2829] BioSQL does not record a generic nucleotide alphabet

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon May 18 10:08:45 UTC 2009


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

           What    |Removed                     |Added
             Status|NEW                         |RESOLVED
         Resolution|                            |WONTFIX

------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-18 06:08 EST -------
(In reply to comment #3)
> Hi
> thank you very much for explaining.
> I'm not sure this is a bug, it's a design feature due to my
> not understanding the implications of generic_nucleotide.  

As I argued on the BioSQL mailing list, generic nucleotide
sequences are a valid case not catered to at the moment.
However, they are a corner case, and have no equivalent in
BioPerl (which is happy to guess at DNA or RNA).

Marking this bug as WON'T FIX.

> I know it's DNA, and if one uses generic_dna instead in
> the testcase, all is well.

Good - if you know you have DNA, then specifying a DNA
alphabet would be my recommended course of action.

> Alphabets are explained clearly in the documentation.
> Thank you again.

Let us know if you find anything that needs further
clarification in the documentation.



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