Juan Manuel Berros jmberros

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jmberros / testing

Created December 10, 2014 16:03

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jmberros / country_from_nuccore_accessions.py

Last active August 25, 2023 06:13

Get the country field for the given nuccore accession numbers.

	from Bio import Entrez

	# Read the accessions from a file
	accessions_file = 'accessions.txt'
	with open(accessions_file) as f:
	ids = f.read().split('\n')

	# Fetch the entries from Entrez
	Entrez.email = '[email protected]' # Insert your email here
	handle = Entrez.efetch('nuccore', id=ids, retmode='xml')

jmberros / tax_ids_to_name_and_lineage.py

Last active November 23, 2016 01:42

Get Taxa scientific name and lineage from Entrez

	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 = '[email protected]' # Put your email here
	handle = Entrez.efetch('taxonomy', id=tax_ids, rettype='xml')
	response = Entrez.read(handle)

jmberros / read_args_from_command_line.py

Last active November 23, 2016 02:07

Read arguments from command line