[Biopython] fetching chromosome sizes without gff file?

[Peter Cock]

Hmm.

Using the NCBI Entrez API, you could certainly download these as
FASTA or GenBank files, either of which would give you the length.
But I don't think that offers GFF files.

I don't work on model organisms, but I'd suggest ENSEMBL might
be a good bet - but we don't yet have a Biopython module for that?

http://www.ensembl.org/
https://github.com/biopython/biopython/issues/512

It might be worth looking at bioservices for this?

https://github.com/cokelaer/bioservices

Peter

On Wed, Mar 22, 2017 at 4:24 PM, Tommy Carstensen
<tommy.carstensen at gmail.com> wrote:
> Is it possible to get the chromosome lengths in maize (Zea mays), zebra fish
> and humans with Biopython without having the relevant gff files? How would I
> go about doing that? Basically I just want to be able to fetch the gff by
> typing in species='homo sapiens' and build=37 or something like that without
> having to worry about URLs.
>
> Could Biopython also give me the position of the pseudoautosomal regions on
> the X chromosome in Homo sapiens?
>
> Thanks,
> Tommy
>
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