[Biopython] Issues parsing genbank files

[David Martin (Staff)]

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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Dr David M A Martin PhD FRSB
Senior Lecturer in Bioinformatics
School of Life Sciences, University of Dundee
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