def test_type(self):
ont = pronto.Ontology()
t1 = pronto.SynonymType("declared", "a declared synonym type")
ont.metadata.synonymtypedefs.add(t1)
term = ont.create_term("TEST:001")
syn = term.add_synonym("something", type=t1)
self.assertEqual(syn.type, t1)
def test_type_setter_undeclared(self):
ont = pronto.Ontology()
ty1 = pronto.SynonymType("undeclared", "an undeclared synonym type")
term = ont.create_term("TEST:001")
syn1 = term.add_synonym("something")
self.assertIsNone(syn1.type)
with self.assertRaises(ValueError):
syn1.type = ty1
def test_type_setter(self):
ont = pronto.Ontology()
ty1 = pronto.SynonymType("declared", "a declared synonym type")
ont.metadata.synonymtypedefs.add(ty1)
term = ont.create_term("TEST:001")
syn1 = term.add_synonym("something")
self.assertIsNone(syn1.type)
syn1.type = ty1
self.assertEqual(syn1.type, ty1)
def test_add_synonym_invalid_type(self):
term = self.ms["MS:1000031"]
st = pronto.SynonymType("undeclared", "an undeclared synonym type")
with self.assertRaises(ValueError):
s = term.add_synonym('instrument type', type=st)
def export_ontos_to_obo(alphabets=None,
filename=None,
_max_monomers=None,
_max_xlinks=None):
""" Exports alphabets of residues and ontology of crosslinks to OBO format
Args:
alphabets (:obj:`list` of :obj:`core.Alphabet`, optional): alphabets to export
filename (:obj:`str`, optional): path to export alphabets
_max_monomers (:obj:`int`, optional): maximum number of monomers to export
_max_xlinks (:obj:`int`, optional): maximum number of crosslinks to export
"""
from .xlink.core import crosslinks_onto
import pronto
if alphabets is None:
alphabets = [
dna.dna_alphabet, rna.rna_alphabet, protein.protein_alphabet
]
if filename is None:
filename = pkg_resources.resource_filename(
'bpforms', os.path.join('alphabet', 'onto.obo'))
# create ontology
onto = pronto.Ontology()
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('structure', 'SMILES-encoded structure', 'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('backbone_bond_atoms', 'Backbone bond atoms',
'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('backbone_displaced_atoms',
'Backbone displaced atoms', 'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('l_bond_atoms', 'Left bond atoms', 'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('l_displaced_atoms', 'Left displaced atoms',
'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('r_bond_atoms', 'Right bond atoms', 'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('r_displaced_atoms', 'Right displaced atoms',
'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('delta_mass', 'Delta mass', 'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('delta_charge', 'Delta charge', 'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('bond_order', 'Bond order', 'EXACT'))
onto.metadata.synonymtypedefs.add(
pronto.SynonymType('bond_stereo', 'Bond stereochemistry', 'EXACT'))
is_a_relationship = onto.get_relationship('is_a')
part_of_relationship = onto.create_relationship('part_of')
derives_from_relationship = onto.create_relationship('derives_from')
l_monomer_relationship = onto.create_relationship('l_monomer')
r_monomer_relationship = onto.create_relationship('r_monomer')
# add terms for monomers to ontology
alphabet_type_term = onto.create_term(id='BpForms:alphabet')
alphabet_type_term.name = 'alphabet'
monomer_type_term = onto.create_term(id='BpForms:monomer')
monomer_type_term.name = 'monomeric form'
monomer_type_term.add_synonym('residue', scope='BROAD')
monomer_type_term.add_synonym('monomer', scope='BROAD')
xlink_type_term = onto.create_term(id='BpForms:crosslink')
xlink_type_term.name = 'crosslink'
monomer_to_term = {}
for alphabet in alphabets:
alphabet_term = onto.create_term(id='BpForms:' + alphabet.id)
alphabet_term.name = alphabet.name
alphabet_term.desc = alphabet.description
alphabet_term.relationships = {
is_a_relationship: [alphabet_type_term],
}
for code, monomer in list(alphabet.monomers.items())[0:_max_monomers]:
synonyms = []
for syn in monomer.synonyms:
synonyms.append(pronto.SynonymData(syn, scope='BROAD'))
for identifier in monomer.identifiers:
synonyms.append(
pronto.SynonymData('{}: {}'.format(identifier.ns,
identifier.id),
scope='EXACT'))
relationships = {
is_a_relationship: [monomer_type_term],
part_of_relationship: [alphabet_term],
}
other = {'structure': [monomer.export('smiles')]}
for atom_type in [
'backbone_bond_atoms', 'backbone_displaced_atoms',
'l_bond_atoms', 'l_displaced_atoms', 'r_bond_atoms',
'r_displaced_atoms'
]:
atoms = getattr(monomer, atom_type)
if atoms:
other[atom_type] = [_atom_to_str(atom) for atom in atoms]
if monomer.delta_mass:
other['delta_mass'] = [monomer.delta_mass]
if monomer.delta_charge:
other['delta_charge'] = [monomer.delta_charge]
term = onto.create_term(
id='BpForms:{}_{}'.format(alphabet.id, code))
term.name = monomer.name or None
term.desc = monomer.comments or ''
term.relationships = relationships
term.other = other
for syn in synonyms:
term.add_synonym(syn.description, scope=syn.scope)
monomer_to_term[monomer] = term
for alphabet in alphabets:
monomer_codes = {
monomer: code
for code, monomer in alphabet.monomers.items()
}
for code, monomer in list(alphabet.monomers.items())[0:_max_monomers]:
monomer_term = onto['BpForms:{}_{}'.format(alphabet.id, code)]
relationships = {}
for base_monomer in monomer.base_monomers:
base_monomer_term = onto.get(
'BpForms:{}_{}'.format(alphabet.id,
monomer_codes[base_monomer]), None)
if base_monomer_term is not None:
relationships[derives_from_relationship] = [
base_monomer_term
]
monomer_term.relationships = relationships
# add terms for crosslinks to ontology
for xlink in list(crosslinks_onto.values())[0:_max_xlinks]:
relationships = {
is_a_relationship: [xlink_type_term],
}
l_monomer_term = monomer_to_term.get(xlink.l_monomer, None)
r_monomer_term = monomer_to_term.get(xlink.r_monomer, None)
if l_monomer_term:
relationships[l_monomer_relationship] = [l_monomer_term]
if r_monomer_term:
relationships[r_monomer_relationship] = [r_monomer_term]
other = {}
for atom_type in [
'l_bond_atoms', 'r_bond_atoms', 'l_displaced_atoms',
'r_displaced_atoms'
]:
other[atom_type] = [
_atom_to_str(atom) for atom in getattr(xlink, atom_type)
]
other['bond_order'] = [xlink.order.name]
if xlink.stereo:
other['bond_stereo'] = [xlink.stereo.name]
term = onto.create_term(id='BpForms:crosslink_{}'.format(xlink.id))
term.name = xlink.name or None
for syn in xlink.synonyms:
term.add_synonym(syn, scope='BROAD')
term.desc = xlink.comments or ''
term.relationships = relationships
term.other = other
# export ontology
with open(filename, 'wb') as file:
onto.dump(file)
def test_type_undeclared(self):
ont = pronto.Ontology()
t1 = pronto.SynonymType("undeclared", "an undeclared synonym type")
term = ont.create_term("TEST:001")
with self.assertRaises(ValueError):
term.add_synonym("something", type=t1)
def test_type(self):
ont = pronto.Ontology()
ty1 = pronto.SynonymType("declared", "a declared synonym type")
ont.metadata.synonymtypedefs.add(ty1)
term = ont.create_term("TEST:001")
term.add_synonym("something", type=ty1)