def test_translate_entrez_symbol(self):
"""
Test translation from entrez to symbol when either standard name or
systematic name is null.
"""
# Test the gene that has standard name.
translation = translate_genes(id_list=[101],
from_id="Entrez",
to_id="Symbol",
organism="Mus computurus")
self.assertEqual(translation, {101: ['std_101'], 'not_found': []})
# Test the gene that does NOT have standard name.
translation = translate_genes(id_list=[102],
from_id="Entrez",
to_id="Symbol",
organism="Mus computurus")
self.assertEqual(translation, {102: ['sys_102'], 'not_found': []})
def test_translate_symbol_entrez_diff_organisms2(self):
"""
Same as previous test, but uses the other organism as input.
"""
translation = translate_genes(id_list=['ACDC'],
from_id="Symbol",
to_id="Entrez",
organism="Monitorus computurus")
self.assertEqual(translation, {'ACDC': [5], 'not_found': []})
def test_translate_symbol_entrez_diff_organisms(self):
"""
translate_genes() should be able to differentiate between different
organism genes when passed identical symbols.
"""
# This test also confirmed that when both standard name and systematic
# name are available, the sysmbol will be standard name.
translation = translate_genes(id_list=['ACDC'],
from_id="Symbol",
to_id="Entrez",
organism="Mus computurus")
self.assertEqual(translation, {'ACDC': [4], 'not_found': []})
def test_translate_entrez_standard_name_missing(self):
"""
Test translation from entrez to standard names with a missing value.
"""
translation = translate_genes(id_list=[1, 2, 3],
from_id="Entrez",
to_id="Standard name")
self.assertEqual(translation, {
1: [
'G1',
],
2: [
'G2',
],
'not_found': [3]
})
def test_translate_entrez_entrez_missing(self):
"""
Test translation from entrez to entrez with a missing value.
"""
translation = translate_genes(id_list=[1, 2, 3],
from_id="Entrez",
to_id="Entrez")
self.assertEqual(translation, {
1: [
1,
],
2: [
2,
],
'not_found': [3]
})
def test_translate_entrez_systematic_name(self):
"""
Test translation from entrez to systematic names.
"""
translation = translate_genes(id_list=[1, 2],
from_id="Entrez",
to_id="Systematic name")
self.assertEqual(translation, {
1: [
'g1',
],
2: [
'g2',
],
'not_found': []
})
def test_translate_entrez_entrez(self):
"""
Test translation from entrez to entrez.
"""
translation = translate_genes(id_list=[1, 2],
from_id="Entrez",
to_id="Entrez")
self.assertEqual(translation, {
1: [
1,
],
2: [
2,
],
'not_found': []
})
def test_translate_entrez_xrdb(self):
"""
Test translation from entrez to ASDF.
"""
translation = translate_genes(id_list=[1, 2],
from_id="Entrez",
to_id="ASDF")
self.assertEqual(translation, {
1: [
'XRID1',
'XRRID1',
],
2: [
'XRID2',
],
'not_found': []
})
def translate_gene_ids(self, request, **kwargs):
self.method_check(request, allowed=['post'])
self.throttle_check(request)
# Extract relevant parameters
gene_list = request.POST.getlist('gene_list')
from_id = request.POST.get('from_id')
to_id = request.POST.get('to_id')
organism = request.POST.get('organism')
# Call the translate_genes method in genes.utils to
# do the actual translating.
return_ids_dict = translate_genes(id_list=gene_list,
from_id=from_id,
to_id=to_id,
organism=organism)
return self.create_response(request, return_ids_dict)
def test_translate_xrdb_entrez(self):
"""
Test translation from ASDF to entrez.
"""
translation = translate_genes(id_list=['XRID1', 'XRRID1', 'XRID2'],
from_id="ASDF",
to_id="Entrez")
self.assertEqual(translation, {
'XRID1': [
1,
],
'XRRID1': [
1,
],
'XRID2': [
2,
],
'not_found': []
})
