Hello Todd,
This sounds a bit like what the biojava BioIndex code does. You make be
able to use that.
- Mark
Todd Riley <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
02/10/2006 12:02 PM
To: biojava-l@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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