def get_duplicates_sequences_ids_by_organism_id(id_organism):
"""
get list of ids of proteins duplicates
:param id_organism: id of the organism
:type id_organism: int - required
:return: list with the proteins ids
:rtype: List((int, int))
"""
list_duplicate_prots_ids = []
list_duplicate_sequence = Protein.get_duplicates_sequence_by_organism_id(
id_organism)
if len(list_duplicate_sequence) > 0:
for sequence, start_point, end_point in list_duplicate_sequence:
if start_point != None and end_point != None:
sqlObj = _Protein_sql_new()
sequence = sequence.replace("'", "")
results = sqlObj.get_protein_id_by_sequence_location(
sequence, start_point, end_point, id_organism)
assert len(results) > 1
default_val = results[0][0]
for element in results[1:]:
list_duplicate_prots_ids.append(
(default_val, element[0]))
else:
with open("proteins_none.txt", "a") as myfile:
myfile.write((str(id_organism) + "," + sequence))
return list_duplicate_prots_ids
def get_protein_id_by_sequence_location(sequence, location_start,
location_end, fk_id_organism):
"""
get id protein with a give sequence, location start and end in a Fk id organism
:param sequence: id of the organism
:param location_start: id of the organism
:param location_end: id of the organism
:param fk_id_organism: id of the organism
:type sequence: int - required
:type location_start: int - required
:type location_end: int - required
:type fk_id_organism: int - required
:return: list with the proteins ids
:rtype: List(int)
"""
list_ids = []
sqlObj = _Protein_sql_new()
results = sqlObj.get_protein_id_by_sequence_location(
sequence, location_start, location_end, fk_id_organism)
for element in results:
list_ids.append(element[0])
return list_ids
def create_protein_all_details_procedure(self, id_organism):
"""
Insert a Protein in the database if it doesn't yet exists and return it id WITHOUT ANY VERIFICATIONS
The protein contains
- accession number
- designation (header)
- proteic sequence
- nucleic sequence
- position start in the gene
- position end in the gene
- position start in the contig
- position end in the contig
- fk_contig
:return: id of the protein
:rtype int
"""
sqlObj = _Protein_sql_new()
id_prot = sqlObj.insert_protein_all_info_return_id_procedure(
self.id_accession, self.designation, self.sequence_prot,
self.sequence_dna, self.start_point, self.end_point,
self.start_point_cnt, self.end_point_cnt, self.fk_id_contig,
id_organism)
self.id_protein = id_prot
return id_prot
def get_id_prot_by_designation(self):
"""
Return the id of the protein given its description
:return: id of the protein
:rtype int
"""
sqlObj = _Protein_sql_new()
id_protein = sqlObj.get_protein_id_by_designation(self.designation)
return id_protein
def remove_protein_by_its_id(id_protein):
"""
remove a protein given its id
:param id_protein: id of the protein
:type id_protein: int - required
:return: prot_dom it removed
:rtype: int
"""
sqlObj = _Protein_sql_new()
id_couple = sqlObj.remove_protein_by_its_id(id_protein)
return id_couple
def get_qty_proteins_by_organism_id(id_organism):
"""
get quantity of proteins given a organism id
:param id_organism: id of the organism
:type id_organism: int - required
:return: quantity of proteins or -1 if unknown the organism
:rtype: int
"""
sqlObj = _Protein_sql_new()
id_couple = sqlObj.get_qty_proteins_by_organism_is(id_organism)
return id_couple
def get_all_Proteins_not_in_temp_prot(self):
"""
return an array with all the Protein in the database which are not in temp_prots (not treated)
:return: array of Protein
:rtype: array(Protein)
"""
listOfProteins = []
sqlObj = _Protein_sql_new()
results = sqlObj.select_all_proteins_not_in_temp_prot()
for element in results:
listOfProteins.append(
Protein(element[0], element[1], element[2], element[3],
element[4], element[5], element[6], element[7],
element[8], element[9]))
return listOfProteins
def get_all_Proteins(self):
"""
return an array with all the Protein in the database
:return: array of Protein
:rtype: array(Protein)
"""
listOfProteins = []
sqlObj = _Protein_sql_new()
results = sqlObj.select_all_proteins_all_attributes()
for element in results:
listOfProteins.append(
Protein(element[0], element[1], element[2], element[3],
element[4], element[5], element[6], element[7],
element[8], element[9]))
return listOfProteins
def update_protein_contig(self):
"""
Update the data of the contig for a given protein id, it updates:
- position start of the contig
- position end of the contig
- FK contig key
:return: if of the updated protein
:rtype int
"""
sqlObj = _Protein_sql_new()
id_prot = sqlObj.set_contig_protein_by_id(self.id_protein,
self.start_point_cnt,
self.end_point_cnt,
self.fk_id_contig)
self.id_protein = id_prot
return id_prot
def get_protein_by_id(id_protein):
"""
return a proteing given its ID
:param id_protein: id of the protein
:type id_protein: int - required
:return: Protein
:rtype: Protein
"""
sqlObj = _Protein_sql_new()
results = sqlObj.select_protein_by_id(id_protein)
protein_obj = Protein(results[0][0], results[0][1], results[0][2],
results[0][3], results[0][4], results[0][5],
results[0][6], results[0][7], results[0][8],
results[0][9])
return protein_obj
def get_duplicates_sequence_by_organism_id(id_organism):
"""
get list of ids of proteins duplicates
:param id_organism: id of the organism
:type id_organism: int - required
:return: list with the proteins ids
:rtype: List((sequence, start_point, end_point))
"""
list_values = []
sqlObj = _Protein_sql_new()
results = sqlObj.get_duplicates_sequences_orga_id(id_organism)
if len(results) > 0:
for element in results:
list_values.append((element[0], element[1], element[2]))
return list_values
else:
return list_values
def create_protein(self):
"""
Insert a Protein in the database if it doesn't yet exists and return it id WITHOUT ANY VERIFICATIONS
The protein contains
- accession number
- designation (header)
- proteic sequence
- nucleic sequence
- position start in the gene
- position end in the gene
:return: id of the protein
:rtype int
"""
sqlObj = _Protein_sql_new()
id_prot = sqlObj.insert_protein_return_id(
self.id_accession, self.designation, self.sequence_prot,
self.sequence_dna, self.start_point, self.end_point)
self.id_protein = id_prot
return id_prot
def get_all_Proteins_limited(quantity_prots, offset_position):
"""
return an array with all the Protein in the database limited by an offset
:param quantity_prots: number of proteins
:param offset_position: where start the collect
:return: array of Protein
:rtype: array(Protein)
"""
listOfProteins = []
sqlObj = _Protein_sql_new()
results = sqlObj.select_all_proteins_all_attributes_limited(
quantity_prots, offset_position)
for element in results:
listOfProteins.append(
Protein(element[0], element[1], element[2], element[3],
element[4], element[5], element[6], element[7],
element[8], element[9]))
return listOfProteins
def get_all_Proteins_by_organism_id(organism_id):
"""
return an array with all the Protein by an organism id
:param organism_id: id of the protein
:type organism_id: int - required
:return: array of Protein
:rtype: array(Protein)
"""
listOfProteins = []
sqlObj = _Protein_sql_new()
results = sqlObj.select_all_proteins_all_attributes_by_organism_id(
organism_id)
for element in results:
listOfProteins.append(
Protein(element[0], element[1], element[2], element[3],
element[4], element[5], element[6], element[7],
element[8], element[9]))
return listOfProteins
def create_protein_secure(self):
"""
Insert a Protein in the database if it doesn't yet exists and return it id, verify if any other protein with the same accession number exists
The protein contains
- accession number
- designation (header)
- proteic sequence
- nucleic sequence
- position start in the gene
- position end in the gene
:return: id of the protein
:rtype int
"""
sqlObj = _Protein_sql_new()
id_protein = sqlObj.get_protein_id_by_accession(self.id_accession)
if id_protein == -1:
id_protein = self.create_protein()
return id_protein
else:
print("It already exists a protein with the accession number n: " +
str(self.id_accession))
return id_protein
