[Biojava-l] fileToBiojava question

[simon rayner]

hi,

can you post the code you are trying to run along with the full error, it
will help to figure out what is happening.  There are now loaders for
biojavax as well, which work well which are available in the biojavax docs
here http://biojava.org/wiki/BioJava:BioJavaXDocs#Example

but yeah, it's confusing unless you happen to be a real java guru.  i keep
having to refer back to the docs because i keep forgeting which class does
what

On Tue, Sep 21, 2010 at 7:46 PM, Bernd Jagla <bernd.jagla at pasteur.fr> wrote:

>  Hello,
>
> 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
> exception:
> 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.
>
> Bernd
>
>
>
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-- 
Simon Rayner

State Key Laboratory of Virology
Wuhan Institute of Virology
Chinese Academy of Sciences
Wuhan, Hubei 430071
P.R.China

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