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 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