[Biojava-l] Large RichSequence collection

[Amr AL-HOSSARY]

If your problem is in parsing/loading all the sequences in memory first,
before managing them, I had created a method public LinkedHashMap<String,S>
process(int max) in Class FastaReader in BioJava 3.0.6. It reads a maximum
(max) sequences to parse, then read next sequenes in a subsequent call.
You can use it. If you need a similar one in Biojava 1, I can make it for
you.

Otherwise, you will need to modify your algorithm to deal with smaller
clusters, based on the task you are doing.

Amr

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Khalil El
Mazouari
Sent: Thursday, August 01, 2013 1:17 AM
To: Biojava-l at lists.open-bio.org
Subject: [Biojava-l] Large RichSequence collection

Hi,

I have to process large dataset of DNA sequence(>= 120.000 seq). Sequences
are first annotated, clustered ... I end up with huge collection of
SimpleRichSequence objects consuming a lot of RAM.

Any suggestion on how to deal effectively with large collection of
RichSequence objects is welcome.

Thanks in advance.

khalil






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