#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of the `pypath` python module
#
# Copyright 2014-2023
# EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
#
# Authors: see the file `README.rst`
# Contact: Dénes Türei (turei.denes@gmail.com)
#
# Distributed under the GPLv3 License.
# See accompanying file LICENSE.txt or copy at
# https://www.gnu.org/licenses/gpl-3.0.html
#
# Website: https://pypath.omnipathdb.org/
#
import csv
import collections
import pypath.resources.urls as urls
import pypath.share.curl as curl
import pypath.share.settings as settings
import pypath.share.common as common
import pypath.utils.mapping as mapping
[docs]
def panglaodb_raw():
"""
Cell type marker genes from PanglaoDB (https://panglaodb.se/index.html).
"""
url = urls.urls['panglaodb']['url']
headers = [settings.get('user_agent')]
c = curl.Curl(url, silent = False, large = True, req_headers = headers)
result = list(csv.DictReader(c.result, delimiter = '\t'))
return result
[docs]
def panglaodb_annotations():
"""
Cell type marker genes from PanglaoDB (https://panglaodb.se/index.html).
"""
to_float = common.float_or_nan
record = collections.namedtuple(
'PanglaodbAnnotation',
(
'canonical_marker',
'cell_type',
'organ',
'germ_layer',
'entity_type',
'human',
'mouse',
'human_sensitivity',
'mouse_sensitivity',
'human_specificity',
'mouse_specificity',
'ubiquitiousness',
'ncbi_tax_id',
)
)
result = collections.defaultdict(set)
raw = panglaodb_raw()
for r in raw:
human = 'Hs' in r['species'],
mouse = 'Mm' in r['species'],
entity_type = 'protein'
uniprots = mapping.map_name(
r['official gene symbol'],
'genesymbol',
'uniprot',
)
this_ncbi_tax_id = 9606
if not uniprots and human:
uniprots = mapping.map_name(
r['official gene symbol'],
'genesymbol',
'trembl',
)
if not uniprots and mouse:
mouse_gs = '-'.join(
x.capitalize()
for x in r['official gene symbol'].split('-')
)
uniprots = mapping.map_name(
mouse_gs,
'genesymbol',
'uniprot',
ncbi_tax_id = 10090,
)
if not uniprots:
uniprots = mapping.map_name(
mouse_gs,
'genesymbol',
'trembl',
ncbi_tax_id = 10090,
)
this_ncbi_tax_id = 10090
if not uniprots and r['gene type'] == 'non-coding RNA':
uniprots = (r['official gene symbol'],)
entity_type = 'lncrna'
for u in uniprots:
result[u].add(
record(
canonical_marker = r['canonical marker'] == '1',
cell_type = r['cell type'],
organ = r['organ'],
germ_layer = r['germ layer'],
entity_type = entity_type, # TODO: handle all entity types
human = human,
mouse = mouse,
human_sensitivity = to_float(r['sensitivity_human']),
mouse_sensitivity = to_float(r['sensitivity_mouse']),
human_specificity = to_float(r['specificity_human']),
mouse_specificity = to_float(r['specificity_mouse']),
ubiquitiousness = to_float(r['ubiquitousness index']),
ncbi_tax_id = this_ncbi_tax_id,
)
)
return result
