[Biojava-l] parse protein sequences in GenBank format

[Matthew Pocock]

Hi Richard,

readGenbank() only deals with DNA, but readGenpept() may do what you 
want. If you can't see this method on SeqIOTools, then you should 
download the recent snapshot release.

Failing that, you can peek into the code for readGenbank() and make a 
copy of that in your own code, replacing the DNATools.getDNA() with 
ProteinTools.getProtein() to make it parse the sequence data as protein.

Matthew

richard cai wrote:
> Hello,
> 
> I am trying to parse a flat file of refseq protein
> sequences in what looks like GenBank format.  However,
> although the program, using SeqIOTools.readGenbank()
> and seq=seqs.nextSequence(), works fine with DNA
> sequences in GenBank format, it fails to extract the
> protein sequences.  Does this method of using
> readGenbank() only deal with DNA sequences?
> 
> Thanks.
> 
> Rich
> 
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