[Biojava-l] Reading Fasta file problem (new to biojava)

[Richard Holland]

You're almost right already - the sample code would be this:

BufferedReader br = new BufferedReader(new FileReader(args[0]));
Namespace ns = RichObjectFactory.getDefaultNamespace();
RichSequenceIterator iterator = RichSequence.IOTools.readFastaProtein(br,ns);

(No need to cast it - it's already a RichSequenceIterator).

The namespace is a hangover from the object model being based on BioSQL, where all sequences belong to a namespace. If you don't care about namespaces (which is highly likely if you're not persisting to BioSQL) then a default one is provided to use as a placeholder, as shown above.

cheers,
Richard

On 16 Dec 2009, at 09:10, Chris Cole wrote:

> [ repost as the first attempt never got through ]
> 
> Hi,
> 
> I'm new to biojava and relatively new to Java, but not new to progamming in general (perl and C).
> 
> As a quick exercise I wanted to be able to read in a Fasta file, but this code here (Solution 2):
> http://biojava.org/wiki/BioJava:Cookbook:SeqIO:ReadFasta
> 
> Has deprecated warnings for SeqIOTools and fileToBioJava(). The code currently works, but what's the non-deprecated way of going about it?
> 
> I can see from Javadoc that RichSequence.IOTools from org.biojavax.bio.seq is now the recommended class, but how does one implement it?
> 
> I've tried this, but readFastaProtein() requires a namespace, which I've no idea what that means.
> BufferedReader br = new BufferedReader(new FileReader(args[0]));
> RichSequenceIterator iter = (RichSequenceIterator)RichSequence.IOTools.readFastaProtein(br);
> 
> All pointers appreciated.
> Cheers,
> Chris
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--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/