Source code for BanzaiDB.fetch

# Copyright 2013 Mitchell Stanton-Cook Licensed under the
# Educational Community License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may
# obtain a copy of the License at
#
# http://www.osedu.org/licenses/ECL-2.0
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# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an "AS IS"
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from Bio import Entrez, SeqIO


[docs]def get_genbank(nucleotide_db_id): """ Given a complete genome identifier (NCBI) return the genome (SeqIO) object """ Entrez.email = "BanzaiDB.user@github.com" handle = Entrez.efetch(db="nucleotide", id=nucleotide_db_id, rettype="gbwithparts") genome = SeqIO.read(handle, "genbank") return genome