Juan Manuel Berros jmberros

## country_from_nuccore_accessions.py
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 = 'name@example.org'  # Insert your email here
handle = Entrez.efetch('nuccore', id=ids, retmode='xml')

## read_args_from_command_line.py
from sys import argv


def main(arg1, arg2):
    # Your logic here
    pass

if __name__ == '__main__':
    main(argv[1], argv[2])

## 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)

## testing
<iframe src='/widget/#{current_client.slug}' style='height: #{height}px; width: 300px;' scrolling='no'></iframe>" %>
	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 = 'name@example.org' # Insert your email here
	handle = Entrez.efetch('nuccore', id=ids, retmode='xml')
	from sys import argv


	def main(arg1, arg2):
	# Your logic here
	pass

	if __name__ == '__main__':
	main(argv[1], argv[2])
	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)