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

[Peter Rice]

Peter C. wrote:

> 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.

For EMBOSS 6.1.0 it should use -sformat refseqp (but will run without
warning after the patch).

For 6.0.1 all you can do is lie and change aa to bp.

We added the protein formats refseqp and genpept in release 6.1.0.
Previous releases warn about the 'aa' tag and continue.

You could run with -nowarning on the command line but we don't recommend
it :-)

regards,

Peter Rice