[Biojava-l] fileToBiojava question

Bernd Jagla bernd.jagla at pasteur.fr
Tue Sep 21 11:46:35 UTC 2010


I am getting a little frustrated with the wiki page (I guess I don't 
spend enough time reading and testing). I have the impression that some 
of the documentation relates to version 3 whereas others relate to 1.5 
or 1.7.
So sorry if this all sounds a bit confused... ;(

I believe I am using 1.7.1. (I wasn't able to find a readme file that 
contains that information) even though I would probably like to use 
version 3. But as I am stuck with an older Eclipse version I think it 
will be even worse when I try that.

Anyways, I am trying to read in sequence files using 
SeqIOTools.fileToBiojava, which seems to be deprecated, with the 
following parameters: "genbank", "dna", bufferedReader.

somehow this works with "fasta" but with genbank I get the following 
Execute failed: Unknown file type '524300'
in some cases I get:
Unknown file type '262156'

Does this mean anything to you?

Or how do you read in a sequence file? I am looking for a generic way 
that covers many file types (genbank, fasta, swissprot...)

Once I have this I will probably be able to get to the feature 
information using the information from the tutorial.

Thanks for your time.


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