[Biopython] large fasta files

[Jurgens de Bruin]

Thanks for all the help much appreciated!


On 9 September 2014 15:04, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Tue, Sep 9, 2014 at 1:55 PM, Jurgens de Bruin <debruinjj at gmail.com>
> wrote:
> > Hi,
> >
> > So the id I am matching to are in a set .
>
> Good :)
>
> > if seq.id in lset_id:
> >    list_seq.append(seq)
>
> This looks like you are building a list of SeqRecord object in memory.
> If you are looking for a large number of entries in the FASTA file, this
> will consume a lot of RAM (and if you run out or RAM will suddenly
> slow down as swap space is used instead).
>
> I would use a generator approach to write out the records you want
> immediately, see the "Filtering a sequence file" example in the
> Cookbook chapter of the Biopython Tutorial:
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>
> In your case, replace "sff" with "fasta" and adjust how the set of
> wanted identifiers is loaded.
>
> Peter
>



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Jurgens de Bruin
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