[Biopython-dev] [Bug 2578] The GenBank SeqRecord parser does not record molecule type or if circular

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http://bugzilla.open-bio.org/show_bug.cgi?id=2578





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2010-12-12 13:58 EST -------
(In reply to comment #3)
> I needed this functionality for my project, and I got what I needed through the
> modified method definition in Bio.GenBank._FeaureConsumer:
> 
>     def residue_type(self, type):
>         """Record the sequence type so we can choose an appropriate alphabet.
>         """
>         self._seq_type = type
>         if 'circular' in type:
>             self.data.annotations['molecule'] = 'circular'
>         else:
>             self.data.annotations['molecule'] = 'linear'
> 
> This obviously doesn't address the need to write GenBank files.
> 

It would be safer to have an elif if 'linear' in type, but sure,
something like that looks sensible. I'd wondered about a boolean
as well (is it circular or not). What's your preference here?


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