Source code for synbiopython.codon.table

Synbiopython (c) Global BioFoundry Alliance 2020

Synbiopython is licensed under the MIT License.

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@author: neilswainston
from collections import defaultdict
import os.path
import re
from urllib.request import urlretrieve

from synbiopython.codon.taxonomy_utils import get_tax_id

_CODON_REGEX = r"([ATGCU]{3}) ([A-Z]|\*) (\d.\d+)"

[docs]def get_table(table_id, dna=True): """Gets a codon table from from supplied parameter, which may be either an organism name or a NCBI Taxonomy id. :param table_id: an organism name or a NCBI Taxonomy id (as either a str or int). :type table_id: str :param dna: boolean parameter specifying whether the codon table returned should contain DNA or RNA codons (default is DNA). :type dna: bool :return: a codon usage table. :rtype: dict """ tax_id = get_tax_id(table_id) results = defaultdict(dict) content = _get_content(tax_id) for vals in sorted(re.findall(_CODON_REGEX, content), key=lambda x: (x[1], x[2])): results[vals[1]][vals[0].replace("U", "T") if dna else vals[0]] = \ float(vals[2]) return dict(results)
def _get_content(tax_id): """Gets Codon Usage Database content, either from cached file or remotely. :param tax_id: a NCBI Taxonomy id. :type tax_id: str :return: the Codon Usage Database content :rtype: str """ target_dir = os.path.join(os.path.expanduser('~'), '.synbiopython/codon') if not os.path.exists(target_dir): os.makedirs(target_dir) target_file = os.path.join(target_dir, "%s.txt" % tax_id) if not os.path.exists(target_file): url = "" + \ "aa=1&style=N&species=%s" % tax_id urlretrieve(url, target_file) with open(target_file) as fle: return