[Bioperl-l] Strange problem with Bio::Seq::LargePrimarySeq]

Stefan Kirov skirov at utk.edu
Mon Mar 14 19:50:04 EST 2005

First you have to answer few questions: how do you get the object?/
use Bio::Seq::LargePrimarySeq does not create an object it merely makes the code available.
/If you post you code here it will be much easier to answer your questions. How do you access the sequence 
(I hope you have read the documentation, which states that it is not generally a good idea to call $seq->seq).
How big is you /tmp? What are trying to accomplish and why you need the whole seq in memory?

I've had the same issue... I ended up breaking down the sequences into
manageable fragments but would really like to get the largePrimarySeq
working.  When I tried loading a chrom size sequence I just sat back
and watched my RAM get used up (2 gigs), then the swap, then the
crash....  So if anyone can help it'd benefit both of us!

Thanks for any help,

On Mon, 14 Mar 2005 16:22:40 -0500, iluminati at earthlink.net <http://portal.open-bio.org/mailman/listinfo/bioperl-l>
<iluminati at earthlink.net <http://portal.open-bio.org/mailman/listinfo/bioperl-l>> wrote:
>/ I'm having this unuusal problem with loading this particular module.  I
/>/ need b/c I'm working with chromosome-sized sequence files as a part of
/>/ my project, but yet it seems to not want to load properly even when it's
/>/ loaded using the following statement:
/>/ use Bio::Seq::LargePrimarySeq;
/>/ I checked my modules, and the necessary module is there.  It seems to
/>/ just not want to load.  Can anyone be of service?
/>/ _______________________________________________
/>/ Bioperl-l mailing list
/>/ Bioperl-l at portal.open-bio.org <http://portal.open-bio.org/mailman/listinfo/bioperl-l>
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