def test_mouse_class1_alleles_H2_Db():
# H2-Db
eq_(parse_allele_name("H2-Db"), AlleleName("H-2", "D", "", "b"))
eq_(normalize_allele_name("H2-Db"), "H-2-Db")
eq_(compact_allele_name("H2-Db"), "Db")
# with hyphen in "H-2"
eq_(parse_allele_name("H-2-Db"), AlleleName("H-2", "D", "", "b"))
eq_(normalize_allele_name("H-2-Db"), "H-2-Db")
eq_(compact_allele_name("H-2-Db"), "Db")
def test_mouse_class2_alleles():
# H2-IAb
eq_(parse_allele_name("H2-IAb"), AlleleName("H-2", "IA", "", "b"))
eq_(normalize_allele_name("H2-IAb"), "H-2-IAb")
eq_(compact_allele_name("H2-IAb"), "IAb")
# with hyphen in "H-2"
eq_(parse_allele_name("H-2-IAb"), AlleleName("H-2", "IA", "", "b"))
eq_(normalize_allele_name("H-2-IAb"), "H-2-IAb")
eq_(compact_allele_name("H-2-IAb"), "IAb")
def test_mouse_class1_alleles_H2_Kk():
# H2-Kk
eq_(parse_allele_name("H2-Kk"), AlleleName("H-2", "K", "", "k"))
eq_(normalize_allele_name("H2-Kk"), "H-2-Kk")
eq_(compact_allele_name("H-2-Kk"), "Kk")
# with a hyphen in "H-2"
eq_(parse_allele_name("H-2-Kk"), AlleleName("H-2", "K", "", "k"))
eq_(normalize_allele_name("H-2-Kk"), "H-2-Kk")
eq_(compact_allele_name("H-2-Kk"), "Kk")
def test_mouse_class1_alleles_H2_Kk():
# H2-Kk
eq_(parse_allele_name("H2-Kk"),
AlleleName("H-2", "K", "", "k"))
eq_(normalize_allele_name("H2-Kk"), "H-2-Kk")
eq_(compact_allele_name("H-2-Kk"), "Kk")
# with a hyphen in "H-2"
eq_(parse_allele_name("H-2-Kk"),
AlleleName("H-2", "K", "", "k"))
eq_(normalize_allele_name("H-2-Kk"), "H-2-Kk")
eq_(compact_allele_name("H-2-Kk"), "Kk")
def test_mouse_class1_alleles_H2_Db():
# H2-Db
eq_(parse_allele_name("H2-Db"),
AlleleName("H-2", "D", "", "b"))
eq_(normalize_allele_name("H2-Db"), "H-2-Db")
eq_(compact_allele_name("H2-Db"), "Db")
# with hyphen in "H-2"
eq_(parse_allele_name("H-2-Db"),
AlleleName("H-2", "D", "", "b"))
eq_(normalize_allele_name("H-2-Db"), "H-2-Db")
eq_(compact_allele_name("H-2-Db"), "Db")
def test_mouse_class2_alleles():
# H2-IAb
eq_(parse_allele_name("H2-IAb"),
AlleleName("H-2", "IA", "", "b"))
eq_(normalize_allele_name("H2-IAb"), "H-2-IAb")
eq_(compact_allele_name("H2-IAb"), "IAb")
# with hyphen in "H-2"
eq_(parse_allele_name("H-2-IAb"),
AlleleName("H-2", "IA", "", "b"))
eq_(normalize_allele_name("H-2-IAb"), "H-2-IAb")
eq_(compact_allele_name("H-2-IAb"), "IAb")
def __init__(self, name: str) -> HLAChain:
"""Create an HLAChain instance.
:param name: the allele name
:type name: str
:return: an HLAChain instance
:rtype: HLAChain
"""
self._name = name
name = mhcnames.parse_allele_name(name)
# extract fields from the name
self._hla_class = self.get_chain_class(name.gene)
self._gene = name.gene
self._allele_group = name.allele_family
self._protein_group = name.allele_code
def get_peptides_bound_by_allele(self,allele_name:str)->pd.DataFrame:
""" returns a subtable contain all info associated with the provided allele_name
:param allele_name: the allele name written in the standard notation
:type allele_name: str
:raises ValueError: incase the provided allele is not in the database
:return: a subtable contain all the experiments associated with the provided allele_name
:rtype: pd.DataFrame
"""
s_allele_name=mhcnames.parse_allele_name(allele_name)
s_allele_name=s_allele_name.gene+'*'+s_allele_name.allele_family+':'+s_allele_name.allele_code
current_alleles=self.get_all_unique_alleles_in_db()
if s_allele_name not in current_alleles:
raise ValueError(f"The provided allele is not currently defined in the database, currently the following is defined: {' ,'.join(current_alleles)}")
return self._database.loc[self._database.allele.contains(s_allele_name),]
def get_frequency_of(self,allele_name:str)->pd.DataFrame:
"""The worker function of the class, Queries AFND for the frequency of the provided allele in different populations
:param allele_name: the allele name in standard notation, for example, A*01:01 or DRB1*15:01
:type allele_name: string
:return: a tuples of two columns, the first contain the country name and the second contains the frequency
:rtype: pd.DataFrame
"""
try:
allele_name=mhcnames.parse_allele_name(allele_name)
except mhcnames.AlleleParseError as exp:
raise ValueError(f'While parsing the provided name: {allele_name} the following error was encountered: {str(exp)}')
q_name = allele_name.gene+'*'+allele_name.allele_family+':'+allele_name.allele_code
try:
print(f'sending the query to the server ....')
response=self._http.request('GET',self._base+q_name)
print(f'response received')
except Exception as exp:
raise RuntimeError(f'While querying the server the following error was encountered: {str(exp)}')
# check that the response is valid
if response.status==404:
raise RuntimeError(f'The provided allele list is not defined in the database, server returned 404 ')
# get the frequency table from the HTML page
html_soup=BeautifulSoup(response.data.decode('utf-8',errors='ignore'),'html.parser')
html_table=html_soup.body.find_all("table")[3].find_all("tr")[1:]
## extract the data from all elements of the table
rows=[]
for row in html_table:
columns=[]
for elem in row:
try:
columns.append(elem.get_text())
except AttributeError:
continue
rows.append(columns)
## create the table
temp_table=pd.DataFrame(data=rows)
freq_table=pd.concat([temp_table.iloc[:,1],temp_table.iloc[:,3]],axis=1)
freq_table.columns=['Country','Frequency']
return freq_table
def test_H2_Kd_without_seps():
eq_(parse_allele_name("H2Kd"), AlleleName("H-2", "K", "", "d"))
def test_H2_Kd_without_seps():
eq_(parse_allele_name("H2Kd"),
AlleleName("H-2", "K", "", "d"))
def test_SLA_1_0101_no_seps():
eq_(
parse_allele_name("SLA-10101"),
AlleleName("SLA", "1", "01", "01"))
def test_SLA_1_HB01():
eq_(
parse_allele_name("SLA-1-HB01"),
AlleleName("SLA", "1", "HB", "01"))
def test_sheep_class1_allele():
eq_(parse_allele_name("Ovar-N*50001"), AlleleName("Ovar", "N", "500",
"01"))
def test_SLA_2_07we01():
eq_(parse_allele_name("SLA-2*07we01"),
AlleleName("SLA", "2", "07we", "01"))
def test_dog_class2_allele():
eq_(parse_allele_name("DLA-DQA1*00101"),
AlleleName("DLA", "DQA1", "01", "01"))
def test_SLA_2_w09pt22():
eq_(parse_allele_name("SLA-2*w09pt22"),
AlleleName("SLA", "2", "w09pt", "22"))
def test_SLA_2_jh01():
eq_(parse_allele_name("SLA-2*jh01"),
AlleleName("SLA", "2", "jh", "01"))
def test_sheep_class2_allele():
eq_(parse_allele_name("Ovar-DRB1*0804"),
AlleleName("Ovar", "DRB1", "08", "04"))
def test_dog_class2_allele():
eq_(parse_allele_name("DLA-DQA1*00101"),
AlleleName("DLA", "DQA1", "01", "01"))