[Biopython] large fasta files

[Jurgens de Bruin]

Hi,

So the id I am matching to are in a set .
if seq.id in lset_id:
   list_seq.append(seq)




On 9 September 2014 14:34, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Tue, Sep 9, 2014 at 1:12 PM, Jurgens de Bruin <debruinjj at gmail.com>
> wrote:
> > Hi,
> >
> > Thanks for the reply I am trying out the
> > Bio.SeqIO.FastaIO.SimpleFastaParser, what I want to achieve is to iterate
> > over the fasta and pull out sequences that are in a predefined list,
> based
> > on id and then write these to a new fasta file.
>
> In that case, the problem could be as simple as using a list
> (slow for large lists) rather than a set (fast) for checking
> membership.
>
> Peter
>



-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20140909/b90b4474/attachment-0001.html>