[Biojava-l] Looking for a RandomAccessFile-like class for sequences

[mark.schreiber at novartis.com]

Hello Todd,

This sounds a bit like what the biojava BioIndex code does. You make be 
able to use that.

- Mark





Todd Riley <toddri at eden.rutgers.edu>
Sent by: biojava-l-bounces at portal.open-bio.org
02/10/2006 12:02 PM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Looking for a RandomAccessFile-like class for sequences


Hello,

I am looking for a RandomAccessFile-like class that can read small, 
arbitrary chunks of a very large (like 250K of human DNA) fasta file. 
(UCSC chromosomal fasta files contain just 1 sequence for the whole 
chromosome).  I was hoping that someone may have already written a class 
that will take in an alphabet and a range (maybe in the form of a 
RangeLocation object) and will return the sequence in that range from 
the file.  I would hate to spend time re-inventing a wheel that may 
already exist.

Thanks,
Todd


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