[Biopython] Download a range from genbank

[Björn Johansson]

thanks! I tried this:

print Entrez.efetch(db ="nucleotide",id = item,rettype = "gb",retmode =
"text", seq_start = 20, seq_stop = 30).read()

and it gives 10 bp of the pUC19 plasmid.

/bjorn



On Tue, Jul 23, 2013 at 1:49 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Tue, Jul 23, 2013 at 10:34 AM, Björn Johansson
> <bjorn_johansson at bio.uminho.pt> wrote:
> > Hi,
> > some genbank records are very large and I am usually only interested in a
> > small part.
> >
> > is it possible to only download a part of a genbank record using
> > Bio.Entrez?
> >
> > cheers,
> > bjorn
>
> Yes, for a sequence database you can use optional arguments to
> the efetch command, see:
> http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
>
> Quote:
>
> seq_start - First sequence base to retrieve. The value should be the
> integer coordinate of the first desired base, with "1" representing
> the first base of the seqence.
>
> seq_stop - Last sequence base to retrieve. The value should be the
> integer coordinate of the last desired base, with "1" representing the
> first base of the seqence.
>
> Peter
>



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