[BioPython] SeqRecord to Genbank: use SeqIO?

Peter biopython at maubp.freeserve.co.uk
Fri Aug 1 09:43:31 UTC 2008


>> I've done a lot of searching and mailing lists, and googling, and surely I
>> must be missing something? What is the simplest way to get a string
>> representing a genbank file, starting with a SeqRecord?
>>
>> I'm sort of shocked that there isn't some sort of SeqRecord.to_genbank()
>> method.
>
> We have discussed something like a SeqRecord.to_format() method (or
> similar name), which would call Bio.SeqIO internally using StringIO
> and return a string.  This fits in nicely with the planned __format__
> and format() functionality in Python 2.6 and 3.0
> http://www.python.org/dev/peps/pep-3101/
>
> See http://portal.open-bio.org/pipermail/biopython-dev/2008-June/003793.html

I've filed this enhancement as Bug 2561 -
http://bugzilla.open-bio.org/show_bug.cgi?id=2561

Any comments or suggestions on the naming of this function could be
recorded there, or discussed on the mailing list.

Peter



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