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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Low-level wrappers around the NCBI E-Utilities. Primarily meant to open
file-like object handles on responses.
"""
import sys
if sys.version_info.major < 3:
from urllib import urlencode
from urllib import urlopen
else:
from urllib.parse import urlencode
from urllib.request import urlopen
from dendropy.utility import textprocessing
ENTREZ_EUTILS_BASE_URL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils"
def efetch(db, ids, rettype, retmode="xml", email=None):
"""
Raw fetch. Returns file-like object opened for reading on string
returned by query.
"""
if textprocessing.is_str_type(ids):
id_list = ids
else:
id_list = ",".join([str(i) for i in set(ids)])
params = {'db': db,
'id': id_list,
'rettype': rettype,
'retmode': retmode}
if email is not None:
params["email"] = email
query_url = ENTREZ_EUTILS_BASE_URL + "/efetch.fcgi?" + urlencode(params)
response = urlopen(query_url)
return response
def get_taxonomy(**kwargs):
params = dict(kwargs)
params["db"] = "taxonomy"
# if "rettype" not in params:
# params["rettype"] = "gbc"
if "retmode" not in params:
params["retmode"] = "xml"
if "email" in kwargs and kwargs["email"] is None:
del params["email"]
query_url = "http://www.ncbi.nlm.nih.gov/sites/entrez?" + urlencode(params)
response = urlopen(query_url)
return response
# # def efetch(db, ids, rettype, retmode="xml", email=None):
# def efetch(db, **kwargs):
# """
# Raw fetch. Returns file-like object opened for reading on string
# returned by query.
# """
# params = dict(kwargs)
# params["db"] = db
# if "email" in kwargs and kwargs["email"] is None:
# del params["email"]
# if "id" in params:
# params["ids"] = params["id"]
# del params["id"]
# if "rettype" not in params:
# params["rettype"] = "gbc"
# if "retmode" not in params:
# params["retmode"] = "xml"
# if "ids" in params:
# ids = params["ids"]
# if textprocessing.is_str_type(ids):
# id_list = ids
# else:
# id_list = ",".join([str(i) for i in list(ids)])
# del params["ids"]
# params["id"] = id_list
# return entrez_get(**params)
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