def build(self, database_connection, **kwargs): kwargs.setdefault('hypothesis_name', self.hypothesis_metadata['name']) task = TextFileGlycanHypothesisSerializer( self.prepare_buffer(), database_connection, **kwargs) task.start() return task
def test_uniprot_info(self): fasta_file = self.setup_tempfile(decorin) glycan_file = self.setup_tempfile(o_glycans) db_file = self.setup_tempfile("") glycan_builder = TextFileGlycanHypothesisSerializer( glycan_file, db_file) glycan_builder.start() glycopeptide_builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer( fasta_file, db_file, glycan_builder.hypothesis_id, protease=['trypsin'], constant_modifications=constant_modifications, variable_modifications=[], max_missed_cleavages=2) glycopeptide_builder.start() post_cleavage = glycopeptide_builder.query(serialize.Peptide).filter( serialize.Peptide.base_peptide_sequence == "DEASGIGPEEHFPEVPEIEPMGPVCPFR").first() self.assertIsNotNone(post_cleavage) self.clear_file(db_file) self.clear_file(fasta_file) self.clear_file(glycan_file)
def test_missing_glycopeptide(self): glycan_file = self.setup_tempfile(o_glycans) fasta_file = self.setup_tempfile(HEPARANASE) db_file = fasta_file + '.db' glycan_builder = TextFileGlycanHypothesisSerializer( glycan_file, db_file) glycan_builder.start() glycopeptide_builder = naive_glycopeptide.FastaGlycopeptideHypothesisSerializer( fasta_file, db_file, glycan_builder.hypothesis_id, protease='trypsin', constant_modifications=constant_modifications, max_missed_cleavages=2) glycopeptide_builder.start() case = glycopeptide_builder.query( Glycopeptide.glycopeptide_sequence == "KFKNSTYS(O-Glycosylation)R{Hex:1; HexNAc:1; Neu5Ac:2}").first() self.assertIsNotNone(case) self.clear_file(glycan_file) self.clear_file(fasta_file) self.clear_file(db_file)
def build(self, database_connection, **kwargs): if kwargs.get('hypothesis_name') is None: kwargs['hypothesis_name'] = (self.hypothesis_metadata['name']) task = TextFileGlycanHypothesisSerializer(load_text(), database_connection, **kwargs) task.start() return task
def build(self, database_connection, **kwargs): if kwargs.get('hypothesis_name') is None: kwargs['hypothesis_name'] = (self.hypothesis_metadata['name']) task = TextFileGlycanHypothesisSerializer( load_text(), database_connection, **kwargs) task.start() return task
def _build_glycan_composition_hypothesis_from_text(database_connection, text_file, hypothesis_name, identifier=None): if hypothesis_name is not None: hypothesis_name = hypothesis_name + '-Glycans' builder = TextFileGlycanHypothesisSerializer( text_file, database_connection, hypothesis_name=hypothesis_name) builder.run() return builder.hypothesis_id
def _build_glycan_composition_hypothesis_from_text(database_connection, text_file, hypothesis_name, identifier=None): if hypothesis_name is not None: hypothesis_name = hypothesis_name + '-Glycans' builder = TextFileGlycanHypothesisSerializer( text_file, database_connection, hypothesis_name=hypothesis_name) builder.run() return builder.hypothesis_id
def glycan_text(context, text_file, database_connection, reduction, derivatization, name): if name is not None: name = validate_glycan_hypothesis_name(context, database_connection, name) click.secho("Building Glycan Hypothesis %s" % name, fg='cyan') reduction = validate_reduction(context, reduction) derivatization = validate_derivatization(context, derivatization) builder = TextFileGlycanHypothesisSerializer( text_file, database_connection, reduction=reduction, derivatization=derivatization, hypothesis_name=name) builder.display_header() builder.start()
def test_throughput(self): fasta_file = fixtures.get_test_data("phil-82-proteins.fasta") glycan_file = fixtures.get_test_data("IAV_matched_glycans.txt") db_file = self.setup_tempfile("") print(db_file) glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, db_file) glycan_builder.start() glycopeptide_builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer( fasta_file, db_file, glycan_builder.hypothesis_id, constant_modifications=constant_modifications, variable_modifications=variable_modifications, max_missed_cleavages=2) glycopeptide_builder.start() self.clear_file(db_file)
def test_extract_forward_backward(self): fasta_file = fixtures.get_test_data("yeast_glycoproteins.fa") glycan_file = self.setup_tempfile(simple_n_glycans) forward_db = self.setup_tempfile("") reverse_db = self.setup_tempfile("") glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, forward_db) glycan_builder.start() builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer( fasta_file, forward_db, 1) cnt = builder.extract_proteins() assert cnt == 251 glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, reverse_db) glycan_builder.start() rev_builder = naive_glycopeptide.ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer( fasta_file, reverse_db, 1) cnt = rev_builder.extract_proteins() assert cnt == 251 fwd_prots = builder.query(serialize.Protein).all() rev_prots = rev_builder.query(serialize.Protein).all() for fx, rx in zip(fwd_prots, rev_prots): assert fx.name == rx.name assert len(fx.glycosylation_sites) == len(rx.glycosylation_sites)
def test_throughput(self): fasta_file = fixtures.get_test_data("phil-82-proteins.fasta") glycan_file = fixtures.get_test_data("IAV_matched_glycans.txt") db_file = self.setup_tempfile("") print(db_file) glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, db_file) glycan_builder.start() glycopeptide_builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer( fasta_file, db_file, glycan_builder.hypothesis_id, constant_modifications=constant_modifications, variable_modifications=variable_modifications, max_missed_cleavages=2) glycopeptide_builder.start() self.clear_file(db_file)
def test_uniprot_info(self): fasta_file = self.setup_tempfile(decorin) glycan_file = self.setup_tempfile(o_glycans) db_file = self.setup_tempfile("") glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, db_file) glycan_builder.start() glycopeptide_builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer( fasta_file, db_file, glycan_builder.hypothesis_id, protease=['trypsin'], constant_modifications=constant_modifications, variable_modifications=[], max_missed_cleavages=2) glycopeptide_builder.start() post_cleavage = glycopeptide_builder.query(serialize.Peptide).filter( serialize.Peptide.base_peptide_sequence == "DEASGIGPEEHFPEVPEIEPMGPVCPFR").first() self.assertIsNotNone(post_cleavage) self.clear_file(db_file) self.clear_file(fasta_file) self.clear_file(glycan_file)
def test_missing_glycopeptide(self): glycan_file = self.setup_tempfile(o_glycans) fasta_file = self.setup_tempfile(HEPARANASE) db_file = fasta_file + '.db' glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, db_file) glycan_builder.start() glycopeptide_builder = naive_glycopeptide.FastaGlycopeptideHypothesisSerializer( fasta_file, db_file, glycan_builder.hypothesis_id, protease='trypsin', constant_modifications=constant_modifications, max_missed_cleavages=2) glycopeptide_builder.start() case = glycopeptide_builder.query( Glycopeptide.glycopeptide_sequence == "KFKNSTYS(O-Glycosylation)R{Hex:1; HexNAc:1; Neu5Ac:2}").first() self.assertIsNotNone(case) self.clear_file(glycan_file) self.clear_file(fasta_file) self.clear_file(db_file)
def test_extract_forward_backward(self): fasta_file = fixtures.get_test_data("yeast_glycoproteins.fa") glycan_file = self.setup_tempfile(simple_n_glycans) forward_db = self.setup_tempfile("") reverse_db = self.setup_tempfile("") glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, forward_db) glycan_builder.start() builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer( fasta_file, forward_db, 1) cnt = builder.extract_proteins() assert cnt == 251 glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, reverse_db) glycan_builder.start() rev_builder = naive_glycopeptide.ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer( fasta_file, reverse_db, 1) cnt = rev_builder.extract_proteins() assert cnt == 251 fwd_prots = builder.query(serialize.Protein).all() rev_prots = rev_builder.query(serialize.Protein).all() for fx, rx in zip(fwd_prots, rev_prots): assert fx.name == rx.name assert len(fx.glycosylation_sites) == len(rx.glycosylation_sites)
def glycan_text(context, text_file, database_connection, reduction, derivatization, name): if name is not None: name = validate_glycan_hypothesis_name(context, database_connection, name) click.secho("Building Glycan Hypothesis %s" % name, fg='cyan') reduction = validate_reduction(context, reduction) derivatization = validate_derivatization(context, derivatization) builder = TextFileGlycanHypothesisSerializer(text_file, database_connection, reduction=reduction, derivatization=derivatization, hypothesis_name=name) builder.display_header() builder.start()