[Biopython] Issues parsing genbank files

[Peter Cock]

I've been off work ill but I saw David's query on Twitter and knew it
was resolved,

https://twitter.com/bioinformagic/status/915326255603552257

I'm not sure if there is an easy way to decide if and when gbwithparts
is essential, or if the NCBI have changed whatever logic controls if
you only a summary? Using gbwithparts is probably a sensible default
if you care about the full sequence and feature list.

David - can you pin point which bit of the Tutorial you'd like this
clarified in please? Its currently written in LaTeX should you want to
submit a pull request directly:

https://github.com/biopython/biopython/tree/master/Doc/Tutorial

Thanks,

Peter

On Wed, Oct 4, 2017 at 7:34 AM, David Martin (Staff)
<d.m.a.martin at dundee.ac.uk> wrote:
> Thanks to Jocelyne for pointing me in the right direction. The answer is to
> use the 'rettype="gbwithparts"' instead of just "gb". This will then
> retrieve the whole record.
>
>
> It would be worth noting this in the Biopython example.
>
>
> ..d
>
>
> Dr David Martin
> Senior Lecturer in Bioinformatics
> College of Life Sciences
> University of Dundee
>
>
>
> ________________________________
> From: Steve Bond <biologyguy at gmail.com>
> Sent: 04 October 2017 01:03
> To: biopython at lists.open-bio.org; David Martin (Staff)
> Subject: Re: [Biopython] Issues parsing genbank files
>
> Hi David,
> This is definitely an issue on NCBI's side. For some reason, trying to pull
> the entire record is causing an error, but you can get the entire record
> minus one residue:
>
> https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_003197.2&seq_start=1&seq_stop=4857449&rettype=gb&retmode=text
>
> It's not restricted to your record either, it seems like anything large is
> causing the issue. Anyway, your work around is to use the seq_stop keyword
> and ask for one fewer residue than the length of the record.
> Maybe you want to let the folks at Entrez know?
> -Steve
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython