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jmberros/tax_ids_to_name_and_lineage.py

Last active November 23, 2016 01:42
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Get Taxa scientific name and lineage from Entrez
Raw
tax_ids_to_name_and_lineage.py
from Bio import Entrez
taxids_filename = '/tmp/taxids.list' # Replace with the path to your Tax IDs file!
with open(taxids_filename) as f:
tax_ids = f.read().split('\n')
Entrez.email = 'user@example.org' # Put your email here
handle = Entrez.efetch('taxonomy', id=tax_ids, rettype='xml')
response = Entrez.read(handle)
for entry in response:
sci_name = entry.get('ScientificName')
lineage_taxa = entry.get('Lineage').split(';')
print(sci_name, ' > '.join(lineage_taxa), sep=',')
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