def protein_number_domains(self):
"""
Count the number of domain for a given protein
:return: the numver of domain
:rtype int
"""
sqlObj = _Prot_dom_sql_new()
value_protdom = sqlObj.count_domains_by_protein_id(self.Fk_id_protein)
if value_protdom == 0:
print("No domains for the protein id: {0}".format(
self.Fk_id_protein))
return value_protdom
def create_protDom_if_not_exist(self):
"""
Insert a ProdDom in the database if it doesn't yet exists and return it id
The ProteinDom contain:
- Id of the protein
- Id of the domain
:return: id ProteinDom
:rtype int
"""
sqlObj = _Prot_dom_sql_new()
value_protdom = sqlObj.insert_protdom_if_not_exist(
self.Fk_id_protein, self.Fk_id_domain)
return value_protdom
def remove_prot_dom_by_protein_id(id_protein):
"""
remove a prot_dom given its protein id
:param id_protein: id of the protein
:type id_protein: int - required
:return: prot_dom it removed
:rtype: int
"""
sqlObj = _Prot_dom_sql_new()
id_couple = sqlObj.remove_prot_dom_by_prot_id(id_protein)
return id_couple
def get_all_protein_domain():
"""
return an array with all the ProtDom in the database
:return: array of ProteinDom
:rtype: array(ProteinDom)
"""
listOfProtDom = []
sqlObj = _Prot_dom_sql_new()
results = sqlObj.select_all_prodom_all_attributes()
for element in results:
listOfProtDom.append(ProteinDom(element[0], element[1],
element[2]))
return listOfProtDom
def get_all_protein_domain_by_protein_id(id_protein):
"""
return an array with all the ProtDom from a protein id
:param id_protein: id of the protein - -1 if unknown
:type id_protein: int - required
:return: array of ProteinDom
:rtype: array(ProteinDom)
"""
listOfProtDom = []
sqlObj = _Prot_dom_sql_new()
results = sqlObj.select_all_prodom_all_attributes_by_protein_id(
id_protein)
for element in results:
listOfProtDom.append(ProteinDom(element[0], element[1],
element[2]))
return listOfProtDom
def get_all_protein_domain_dict():
"""
return an array with all the ProtDom in the database in a dictionary with ['id_protein']:id_domain
:return: dictionary of ProteinDom
:rtype: dict(id_prot:id_dom)
"""
dict_protein = defaultdict(list)
sqlObj = _Prot_dom_sql_new()
results = sqlObj.select_all_prodom_all_attributes()
for element in results:
dict_protein[element[1]].append(element[2])
#if element[1] in dict_protein.keys():
# print(element[2])
# dict_protein[element[1]] = dict_protein[element[1]].append(element[2])
#else:
# dict_protein[element[1]] = [element[2]]
return dict_protein