def test_parse_target(self):
spaced = 'Q @ N-term'
part_spaced = 'Q @N-Term'
part_spaced2 = 'Q@ n-term'
no_space = 'Q@N-term'
spaced_parsed = modification.extract_targets_from_string(spaced)
self.assertEqual(spaced_parsed, modification.extract_targets_from_string(part_spaced))
self.assertEqual(spaced_parsed, modification.extract_targets_from_string(part_spaced2))
self.assertEqual(spaced_parsed, modification.extract_targets_from_string(no_space))
def transform_modification(mod):
if isinstance(mod, basestring):
mod_inst = modification.Modification(mod)
target = modification.extract_targets_from_string(mod)
new_rule = mod_inst.rule.clone({target})
return new_rule
return mod
def add_modification():
name = request.values.get("new-modification-name")
formula = request.values.get("new-modification-formula")
target = request.values.get("new-modification-target")
if name is None or name == "":
g.add_message("Modification Name Cannot Be Empty")
return abort(400)
try:
composition = Composition(str(formula))
except ChemicalCompositionError:
g.add_message("Invalid Formula")
return abort(400)
try:
target = extract_targets_from_string(target)
except Exception:
g.add_message("Invalid Target Specification")
return abort(400)
rule = ModificationRule(target, name, None, composition.mass, composition)
try:
add_user_peptide_modification_rule(rule)
except Exception:
g.add_message("Failed to save modification rule")
return abort(400)
return jsonify(name=rule.name,
formula=formula,
mass=rule.mass,
specificities=list(rule.as_spec_strings()))
def parse_peptide_modification_target_spec(context, spec_string_list):
out = []
for spec_string in spec_string_list:
try:
spec = extract_targets_from_string(spec_string)
out.append(spec)
except Exception as e:
raise ValueError(str(e))
return out