[emboss-dev] Regression in GenBank/GenPept parsing?

Peter biopython at maubp.freeserve.co.uk
Tue Jul 21 13:21:46 UTC 2009

Peter C. wrote:
> Peter Rice wrote:
>> Peter C. wrote:
>>> Great. This may save you having to answer my next question,
>>> which was could you expand on what EMBOSS considers to be
>>> the differences between "genbank", "genpept" and "refseqp" as
>>> file formats? Of course, I may come up with further questions ;)
>> Oh, further questions please! We love answering them.
>> GenPept format expects to find 9 fields on the LOCUS line.
>> RefseqP format expects only 8.
>> The difference is GenPept format including the original GenPept locus name.
> Which 8 or 9 fields?

Oh, and a related question: Can I adjust the GenPept file in question
(emailed to Peter Rice off list) to get rid of the warning from
EMBOSS 6.0.1 about the bad LOCUS line? If there is something
wrong with the GenBank/GenPept LOCUS lines Biopython writes,
I'd like to fix it before our next release.

Peter C.

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