[Biojava-l] Re: [Biojava-dev] Initial impressions...

[Len Trigg]

Matthew Pocock wrote:
> We need to make this process much easier. Unfortunately, getAsChar() 
> doesn't realy work for us because we can have symbols for things that 
> don't have a single char representation, such as codons. However, you 
> shouldn't have to end up going through 20 function calls either.
> 
> Is there a biojava in anger example of geting letters from symbols?

Nope, not that I could see. BTW, the BioJava in Anger is a very
helpful document, I've been consulting it often :-). Sounds like this
would make a good addition to the "how do I get between strings and
symbols" section.

On a related note, biojava seems to always use lowercase when writing
out DNA sequences. Is there an officially endorsed method for
switching to upper case? Should I modify my AlphabetManager.xml, or
should I reregister a new CharacterTokenization with the name "token"
so that it overrides the default one and gets picked by the various
output formats?


> > Parsing a BLAST output file was also easy, however, I had to use
> > "lazy" mode to work with our files (from NCBI BLAST 2.2.1), and I have
> > not yet figured out how to extract a) the length of the query
> > sequence, and b) the frame of the hits. Any suggestions here?
> 
> Is that information in the annotation attached to the 
> SeqSimilaritySearchSubHit or the SeqSimilritySearchResult?

When I print out all the annotations (basically using the BIA example
BlastParser.java, modified to include sub hit information), I see that
the queryFrame is present, but the query length information is not.



> Good luck with BioSQL and GFF. These are parts of the library that I use 
> daily. Oh, and for the GFF, start off by using GFFTools.

I've written some sequences, annotated from GFF files to a mysql
database using BioSQL, and it worked great! Does the BioJava code
support writing taxonomy information to the database, so I can link my
sequences to species?


(I've moved this to biojava-l, since this seems more of a biojava-l
question than biojava-dev question, although with open source class
libraries, the line often seems to get blurred :-))

Cheers,
Len.