Entrez.efetch
helpfully gives me the feature table of a nuccore entry.
If I understand correctly, efetch
can only return the feature table in a textual format (e.g., as mentioned here).
Is there any built-in Python/Biopython function that parses this textual format of a feature table?
Here is a code snippet that uses efetch
and writes the feature table to a file:
from Bio import Entrez
Entrez.email = "[email protected]"
with Entrez.efetch(db='nuccore', id='U00096.3', rettype='ft') as handle:
feature_table = handle.read()
with open('feature_table.txt', 'w') as f:
f.write(feature_table)
Here are the first 20 lines of feature_table.txt
:
>Feature gb|U00096.3|
190 255 gene
gene thrL
gene_syn ECK0001
locus_tag b0001
db_xref ASAP:ABE-0000006
db_xref ECOCYC:EG11277
db_xref EcoGene:EG11277
190 255 CDS
product thr operon leader peptide
transl_table 11
protein_id gb|AAC73112.1|
transcript_id gnl|b0001|mrna.b0001
db_xref UniProtKB/Swiss-Prot:P0AD86
337 2799 gene
gene thrA
gene_syn ECK0002
gene_syn Hs
gene_syn thrA1
gene_syn thrA2