def to_comet_parameter(self) -> str:
"""
Returns the modifications as comet parameter. If the the modification is static, the result is ready to use.
If the modification is variable or terminus modification, the resulting string contains a placeholder ('|i') for the variable modification index and another one ('|v') for the variable modification maximum.
Remember Comet allows only 9 variable modifications in total.
Returns
-------
Mostly ready to use Comet configuration string of the modification
"""
if self.is_static and not self.is_terminus_modification:
return "add_{}_{} = {}".format(self.amino_acid.one_letter_code, self.amino_acid.name.lower().replace(" ", "_"), mass_to_float(self.delta))
elif self.is_static and self.is_position_n_terminus:
return "add_Nterm_peptide = {}".format(mass_to_float(self.delta))
elif self.is_static and self.is_position_c_terminus:
return "add_Cterm_peptide = {}".format(mass_to_float(self.delta))
elif self.is_variable and not self.is_terminus_modification:
return "variable_mod0|i = {} {} 0 |v -1 2 0 0.0".format(
mass_to_float(self.delta),
self.amino_acid.one_letter_code
)
elif self.is_variable and self.is_position_n_terminus:
return "variable_mod0|i = {} {} 0 |v 0 2 0 0.0".format(
mass_to_float(self.delta),
self.amino_acid.one_letter_code
)
elif self.is_variable and self.is_position_c_terminus:
return "variable_mod0|i = {} {} 0 |v 0 3 0 0.0".format(
mass_to_float(self.delta),
self.amino_acid.one_letter_code
)
def to_csv_row(self) -> Iterator[ByteString]:
"""
Yields the peptide as CSV row
Yields
------
Iterator[ByteString]
CSV row with 2 or 7 columns, depending if the peptide was queried with metadata
"""
yield str(mass_to_float(self.mass)).encode("utf-8")
# At this point only string values are added to the cssv, so we quote them for better compatibility
yield b",\""
yield self.sequence.encode("utf-8")
yield b"\","
yield str(self.number_of_missed_cleavages).encode("utf-8")
def __str__(self):
result = ""
for combination in self.__modification_collection_list:
mass = ""
amino_acid_counts = []
for condition in combination.where_conditions:
if not self.__with_partition and condition.column_name == "partition":
continue
output = f"{condition.column_name} {condition.operator}"
if condition.column_name == "mass":
mass = output % tuple(
[mass_to_float(mass) for mass in condition.values])
else:
amino_acid_counts.append(output % condition.values)
amino_acid_counts.sort()
result += f"{mass} ({' & '.join(amino_acid_counts)})"
result += "\n"
return result.replace(" BETWEEN", ":").replace("AND", "-")
def to_json(self, close: bool = True) -> Iterator[ByteString]:
"""
Generator which yields the peptides as a json formatted string
Arguments
---------
close : bool
If true a closing bracket is added, default True
Yields
------
Iterator[ByteString]
JSON formatted string.
"""
yield b"{\"mass\":"
yield str(mass_to_float(self.mass)).encode("utf-8")
yield b",\"sequence\":\""
yield self.sequence.encode("utf-8")
yield b"\",\"length\":"
yield str(self.length).encode("utf-8")
yield b",\"number_of_missed_cleavages\":"
yield str(self.number_of_missed_cleavages).encode("utf-8") #
if close:
yield b"}"
def sequence_mass(sequence):
peptide = Peptide(sequence, 0)
return jsonify({'mass': mass_to_float(peptide.mass)})