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 > > __________________________________________________ > Do You Yahoo!? > Yahoo! Finance - Get real-time stock quotes > http://finance.yahoo.com > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
