[EMBOSS] seqret: warnings with refseq format

Peter Rice pmr at ebi.ac.uk
Tue Oct 7 10:44:56 UTC 2008

Dear Oliver,

Oliver Wafzig wrote:
> Using the following command to convert a 'RefSeq' protein file to fasta,
> I get a lot of warnings about "bad Genbank LOCUS line".
> 	seqret -nofeature -sequence rsnc.0312.2008.gpff  -nofirstonly
> -outseq fasta::stdout
> I tested it with version 5.0.0 and the current stable 6.0.1 emboss
> package.
> Is that a known issue?

Thanks for pointing it out. It is some time since I looked at refseq and 
nobody has reported this one.

We define refseq as using GenBank format. We need to make a separate 
Refseq parser (copy the GenBank one and fix the messages). Not hard to do.


Peter Rice

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