[Biopython] Issues parsing genbank files

[Jocelyne]

Hi David:
I think if you are searching by id, you should only get 1 record.
The questions you are asking sound to me like Entrez / NCBI databases
questions, not necessarily Biopython questions. Unless someone else has
time to dive into your specific example, I suggest you look at this
documentation:
https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Entrez/
https://www.ncbi.nlm.nih.gov/books/NBK25501/
Jocelyne





On Tue, Oct 3, 2017 at 2:39 AM, David Martin (Staff) <
d.m.a.martin at dundee.ac.uk> wrote:

> Hi folks,
>
>
>
> I’m trying to parse some bacterial genomes. I’ve lifted the following code
> from the biopython tutorial but it seems to be giving issues.
>
>
>
> from Bio import Entrez
>
> from Bio import SeqIO
>
> Entrez.email = "A.N.Other at example.com"
>
> with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text",
> id="nc_003197") as handle:
>
>     seq_record = SeqIO.read(handle, "gb") #using "gb" as an alias for
> "genbank"
>
> print("%s with %i features" % (seq_record.id, len(seq_record.features)))
>
>
>
> I get one feature instead of the thousands expected.
>
>
>
> Trying to extract a single gene I get a run of NN instead of sequence.
>
>
>
> Thoughts: This is initially retrieved as a set of annotations but no
> sequence. Is there a way to ensure entrez retrieves the full data?
>
>
>
> ..d
>
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