def glycopeptide_mzid(context, mzid_file, database_connection, name, occupied_glycosites, target_protein,
target_protein_re, processes, glycan_source, glycan_source_type, glycan_source_identifier,
reference_fasta, peptide_length_range=(5, 60)):
'''Constructs a glycopeptide hypothesis from a MzIdentML file of proteins and a
collection of glycans.
'''
proteins = validate_mzid_proteins(
context, mzid_file, target_protein, target_protein_re)
validate_glycan_source(context, database_connection,
glycan_source, glycan_source_type,
glycan_source_identifier)
processes = min(multiprocessing.cpu_count(), processes)
if name is not None:
name = validate_glycopeptide_hypothesis_name(
context, database_connection, name)
click.secho("Building Glycopeptide Hypothesis %s" % name, fg='cyan')
glycan_hypothesis_id = _glycan_hypothesis_builders[
glycan_source_type](database_connection, glycan_source, name, glycan_source_identifier)
builder = MultipleProcessMzIdentMLGlycopeptideHypothesisSerializer(
mzid_file, database_connection,
glycan_hypothesis_id=glycan_hypothesis_id,
hypothesis_name=name,
target_proteins=proteins,
max_glycosylation_events=occupied_glycosites,
reference_fasta=reference_fasta,
n_processes=processes)
builder.display_header()
builder.start()
return builder.hypothesis_id
def glycopeptide_mzid(context, mzid_file, database_connection, name,
occupied_glycosites, target_protein, target_protein_re,
processes, glycan_source, glycan_source_type,
glycan_source_identifier, reference_fasta):
'''Constructs a glycopeptide hypothesis from a MzIdentML file of proteins and a
collection of glycans.
'''
proteins = validate_mzid_proteins(context, mzid_file, target_protein,
target_protein_re)
validate_glycan_source(context, database_connection, glycan_source,
glycan_source_type, glycan_source_identifier)
processes = min(multiprocessing.cpu_count(), processes)
if name is not None:
name = validate_glycopeptide_hypothesis_name(context,
database_connection, name)
click.secho("Building Glycopeptide Hypothesis %s" % name, fg='cyan')
glycan_hypothesis_id = _glycan_hypothesis_builders[glycan_source_type](
database_connection, glycan_source, name, glycan_source_identifier)
builder = MultipleProcessMzIdentMLGlycopeptideHypothesisSerializer(
mzid_file,
database_connection,
glycan_hypothesis_id=glycan_hypothesis_id,
hypothesis_name=name,
target_proteins=proteins,
max_glycosylation_events=occupied_glycosites,
reference_fasta=reference_fasta,
n_processes=processes)
builder.display_header()
builder.start()
return builder.hypothesis_id
def glycopeptide_fa(context, fasta_file, database_connection, enzyme, missed_cleavages, occupied_glycosites, name,
constant_modification, variable_modification, processes, glycan_source, glycan_source_type,
glycan_source_identifier=None, semispecific_digest=False, reverse=False, dry_run=False,
peptide_length_range=(5, 60), not_full_crossproduct=False):
'''Constructs a glycopeptide hypothesis from a FASTA file of proteins and a
collection of glycans.
'''
if reverse:
task_type = ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer
click.secho("Using ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer", fg='yellow')
elif dry_run:
task_type = NonSavingMultipleProcessFastaGlycopeptideHypothesisSerializer
click.secho("Using NonSavingMultipleProcessFastaGlycopeptideHypothesisSerializer", fg='yellow')
else:
task_type = MultipleProcessFastaGlycopeptideHypothesisSerializer
validate_modifications(
context, constant_modification + variable_modification)
validate_glycan_source(context, database_connection,
glycan_source, glycan_source_type,
glycan_source_identifier)
processes = min(multiprocessing.cpu_count(), processes)
if name is not None:
name = validate_glycopeptide_hypothesis_name(
context, database_connection, name)
click.secho("Building Glycopeptide Hypothesis %s" % name, fg='cyan')
mt = RestrictedModificationTable(
None, constant_modification, variable_modification)
constant_modification = [mt[c] for c in constant_modification]
variable_modification = [mt[c] for c in variable_modification]
glycan_hypothesis_id = _glycan_hypothesis_builders[
glycan_source_type](database_connection, glycan_source, name, glycan_source_identifier)
builder = task_type(
fasta_file, database_connection,
glycan_hypothesis_id=glycan_hypothesis_id,
protease=enzyme,
constant_modifications=constant_modification,
variable_modifications=variable_modification,
max_missed_cleavages=missed_cleavages,
max_glycosylation_events=occupied_glycosites,
hypothesis_name=name,
semispecific=semispecific_digest,
n_processes=processes,
full_cross_product=not not_full_crossproduct)
builder.display_header()
builder.start()
return builder.hypothesis_id
def mzid_glycopeptide(database_connection, mzid_file, name, occupied_glycosites, target_protein,
processes, glycan_source, glycan_source_type, glycan_source_identifier,
channel):
context = None
proteins = validate_mzid_proteins(
context, mzid_file, target_protein, [])
try:
validate_glycan_source(context, database_connection,
glycan_source, glycan_source_type,
glycan_source_identifier)
except Abort:
channel.abort("Could not validate the glycan source, %s, %s" % (glycan_source, glycan_source_type))
if name is not None:
name = validate_glycopeptide_hypothesis_name(
context, database_connection, name)
glycan_hypothesis_id = _glycan_hypothesis_builders[
glycan_source_type](database_connection, glycan_source,
name, glycan_source_identifier)
builder = MultipleProcessMzIdentMLGlycopeptideHypothesisSerializer(
mzid_file, database_connection,
glycan_hypothesis_id=glycan_hypothesis_id,
hypothesis_name=name,
target_proteins=proteins,
max_glycosylation_events=occupied_glycosites,
n_processes=processes)
try:
builder.start()
record = project_hypothesis.HypothesisRecordSet(database_connection)
hypothesis_record = None
for item in record:
if item.uuid == builder.hypothesis.uuid:
hypothesis_record = item
hypothesis_record = hypothesis_record._replace(user_id=channel.user.id)
channel.send(Message(hypothesis_record.to_json(), "new-hypothesis"))
break
else:
channel.send(Message("Something went wrong (%r)" % (list(record),)))
except Exception:
channel.abort(Message.traceback())
def fasta_glycopeptide(database_connection, fasta_file, enzyme,
missed_cleavages, occupied_glycosites, name,
constant_modification, variable_modification, processes,
glycan_source, glycan_source_type,
glycan_source_identifier, peptide_length_range,
semispecific_digest, generate_full_crossproduct,
generate_reverse_decoys, channel):
context = None
try:
validate_modifications(context,
constant_modification + variable_modification)
except Exception:
channel.abort(
"Could not validate the modification specification, Constant: %s, Variable: %s"
% (constant_modification, variable_modification))
try:
validate_glycan_source(context, database_connection, glycan_source,
glycan_source_type, glycan_source_identifier)
except Abort:
channel.abort("Could not validate the glycan source, %s, %s" %
(glycan_source, glycan_source_type))
if name is not None:
name = validate_glycopeptide_hypothesis_name(context,
database_connection, name)
mt = RestrictedModificationTable(None, constant_modification,
variable_modification)
constant_modification = [mt[c] for c in constant_modification]
variable_modification = [mt[c] for c in variable_modification]
glycan_hypothesis_id = _glycan_hypothesis_builders[glycan_source_type](
database_connection, glycan_source, name, glycan_source_identifier)
builder = MultipleProcessFastaGlycopeptideHypothesisSerializer(
fasta_file,
database_connection,
glycan_hypothesis_id=glycan_hypothesis_id,
protease=enzyme,
constant_modifications=constant_modification,
variable_modifications=variable_modification,
max_missed_cleavages=missed_cleavages,
max_glycosylation_events=occupied_glycosites,
hypothesis_name=name,
peptide_length_range=peptide_length_range,
semispecific=semispecific_digest,
n_processes=processes,
full_cross_product=generate_full_crossproduct)
decoy_builder = None
decoy_database_connection = None
if generate_reverse_decoys:
prefix, ext = database_connection.rsplit(".", 1)
decoy_database_connection = "%s.decoy.%s" % (prefix, ext)
try:
validate_glycan_source(context, decoy_database_connection,
glycan_source, glycan_source_type,
glycan_source_identifier)
except Abort:
channel.abort("Could not validate the glycan source, %s, %s" %
(glycan_source, glycan_source_type))
decoy_glycan_hypothesis_id = _glycan_hypothesis_builders[
glycan_source_type](decoy_database_connection, glycan_source, name,
glycan_source_identifier)
decoy_builder = ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer(
fasta_file,
decoy_database_connection,
glycan_hypothesis_id=decoy_glycan_hypothesis_id,
protease=enzyme,
constant_modifications=constant_modification,
variable_modifications=variable_modification,
max_missed_cleavages=missed_cleavages,
max_glycosylation_events=occupied_glycosites,
hypothesis_name=name,
peptide_length_range=peptide_length_range,
semispecific=semispecific_digest,
n_processes=processes,
full_cross_product=generate_full_crossproduct)
try:
builder.start()
record = project_hypothesis.HypothesisRecordSet(database_connection)
hypothesis_record = None
decoy_hypothesis_record = None
if decoy_builder:
decoy_builder.start()
decoy_record = project_hypothesis.HypothesisRecordSet(
decoy_database_connection)
for item in decoy_record:
if item.uuid == decoy_builder.hypothesis.uuid:
decoy_hypothesis_record = item._replace(
user_id=channel.user.id,
options={
'full_crossproduct': generate_full_crossproduct
})
break
else:
channel.send(
Message("Something went wrong (%r)" % (list(record), )))
channel.abort("Could not extract decoy hypothesis")
for item in record:
if item.uuid == builder.hypothesis.uuid:
hypothesis_record = item
hypothesis_record = hypothesis_record._replace(
user_id=channel.user.id,
options={'full_crossproduct': generate_full_crossproduct})
if decoy_hypothesis_record is not None:
hypothesis_record = hypothesis_record._replace(
decoy_hypothesis=decoy_hypothesis_record)
channel.send(
Message(hypothesis_record.to_json(), "new-hypothesis"))
break
else:
channel.send(
Message("Something went wrong (%r)" % (list(record), )))
except Exception:
channel.send(Message.traceback())
def mzid_glycopeptide(database_connection, mzid_file, name,
occupied_glycosites, target_protein, processes,
glycan_source, glycan_source_type,
glycan_source_identifier, peptide_length_range,
generate_full_crossproduct, generate_reverse_decoys,
channel):
context = None
proteins = validate_mzid_proteins(context, mzid_file, target_protein, [])
try:
validate_glycan_source(context, database_connection, glycan_source,
glycan_source_type, glycan_source_identifier)
except Abort:
channel.abort("Could not validate the glycan source, %s, %s" %
(glycan_source, glycan_source_type))
if name is not None:
name = validate_glycopeptide_hypothesis_name(context,
database_connection, name)
glycan_hypothesis_id = _glycan_hypothesis_builders[glycan_source_type](
database_connection, glycan_source, name, glycan_source_identifier)
builder = MultipleProcessMzIdentMLGlycopeptideHypothesisSerializer(
mzid_file,
database_connection,
glycan_hypothesis_id=glycan_hypothesis_id,
hypothesis_name=name,
target_proteins=proteins,
max_glycosylation_events=occupied_glycosites,
peptide_length_range=peptide_length_range,
n_processes=processes,
full_cross_product=generate_full_crossproduct)
decoy_builder = None
decoy_database_connection = None
if generate_reverse_decoys:
# TODO Implement reversing mzIdentML database build
prefix, ext = database_connection.rsplit(".", 1)
decoy_database_connection = "%s.decoy.%s" % (prefix, ext)
try:
validate_glycan_source(context, decoy_database_connection,
glycan_source, glycan_source_type,
glycan_source_identifier)
except Abort:
channel.abort("Could not validate the glycan source, %s, %s" %
(glycan_source, glycan_source_type))
channel.abort("Cannot build a reversed mzIdentML hypothesis")
# decoy_glycan_hypothesis_id = _glycan_hypothesis_builders[
# glycan_source_type](decoy_database_connection, glycan_source,
# name, glycan_source_identifier)
# decoy_builder = ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer(
# mzid_file, decoy_database_connection,
# glycan_hypothesis_id=decoy_glycan_hypothesis_id,
# max_glycosylation_events=occupied_glycosites,
# hypothesis_name="Reverse " + name,
# peptide_length_range=peptide_length_range,
# n_processes=processes,
# full_cross_product=full_cross_product)
try:
builder.start()
record = project_hypothesis.HypothesisRecordSet(database_connection)
hypothesis_record = None
decoy_hypothesis_record = None
if decoy_builder:
decoy_builder.start()
decoy_record = project_hypothesis.HypothesisRecordSet(
decoy_database_connection)
for item in decoy_record:
if item.uuid == decoy_builder.hypothesis.uuid:
decoy_hypothesis_record = item
decoy_hypothesis_record = decoy_hypothesis_record._replace(
user_id=channel.user.id,
options={
'full_cross_product': generate_full_crossproduct
})
break
for item in record:
if item.uuid == builder.hypothesis.uuid:
hypothesis_record = item
hypothesis_record = hypothesis_record._replace(
user_id=channel.user.id,
options={'full_cross_product': generate_full_crossproduct})
if decoy_hypothesis_record is not None:
hypothesis_record = hypothesis_record._replace(
decoy_hypothesis=decoy_hypothesis_record)
channel.send(
Message(hypothesis_record.to_json(), "new-hypothesis"))
break
else:
channel.send(
Message("Something went wrong (%r)" % (list(record), )))
except Exception:
channel.abort(Message.traceback())
def glycopeptide_fa(context,
fasta_file,
database_connection,
enzyme,
missed_cleavages,
occupied_glycosites,
name,
constant_modification,
variable_modification,
processes,
glycan_source,
glycan_source_type,
glycan_source_identifier=None,
reverse=False,
dry_run=False):
'''Constructs a glycopeptide hypothesis from a FASTA file of proteins and a
collection of glycans.
'''
if reverse:
task_type = ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer
click.secho(
"Using ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer",
fg='yellow')
elif dry_run:
task_type = NonSavingMultipleProcessFastaGlycopeptideHypothesisSerializer
click.secho(
"Using NonSavingMultipleProcessFastaGlycopeptideHypothesisSerializer",
fg='yellow')
else:
task_type = MultipleProcessFastaGlycopeptideHypothesisSerializer
validate_modifications(context,
constant_modification + variable_modification)
validate_glycan_source(context, database_connection, glycan_source,
glycan_source_type, glycan_source_identifier)
processes = min(multiprocessing.cpu_count(), processes)
if name is not None:
name = validate_glycopeptide_hypothesis_name(context,
database_connection, name)
click.secho("Building Glycopeptide Hypothesis %s" % name, fg='cyan')
mt = RestrictedModificationTable(None, constant_modification,
variable_modification)
constant_modification = [mt[c] for c in constant_modification]
variable_modification = [mt[c] for c in variable_modification]
glycan_hypothesis_id = _glycan_hypothesis_builders[glycan_source_type](
database_connection, glycan_source, name, glycan_source_identifier)
builder = task_type(fasta_file,
database_connection,
glycan_hypothesis_id=glycan_hypothesis_id,
protease=enzyme,
constant_modifications=constant_modification,
variable_modifications=variable_modification,
max_missed_cleavages=missed_cleavages,
max_glycosylation_events=occupied_glycosites,
hypothesis_name=name,
n_processes=processes)
builder.display_header()
builder.start()
return builder.hypothesis_id
def fasta_glycopeptide(database_connection, fasta_file, enzyme,
missed_cleavages, occupied_glycosites, name,
constant_modification, variable_modification, processes,
glycan_source, glycan_source_type,
glycan_source_identifier, channel):
context = None
try:
validate_modifications(context,
constant_modification + variable_modification)
except Exception:
channel.abort(
"Could not validate the modification specification, Constant: %s, Variable: %s"
% (constant_modification, variable_modification))
try:
validate_glycan_source(context, database_connection, glycan_source,
glycan_source_type, glycan_source_identifier)
except Abort:
channel.abort("Could not validate the glycan source, %s, %s" %
(glycan_source, glycan_source_type))
if name is not None:
name = validate_glycopeptide_hypothesis_name(context,
database_connection, name)
mt = RestrictedModificationTable(None, constant_modification,
variable_modification)
constant_modification = [mt[c] for c in constant_modification]
variable_modification = [mt[c] for c in variable_modification]
glycan_hypothesis_id = _glycan_hypothesis_builders[glycan_source_type](
database_connection, glycan_source, name, glycan_source_identifier)
builder = MultipleProcessFastaGlycopeptideHypothesisSerializer(
fasta_file,
database_connection,
glycan_hypothesis_id=glycan_hypothesis_id,
protease=enzyme,
constant_modifications=constant_modification,
variable_modifications=variable_modification,
max_missed_cleavages=missed_cleavages,
max_glycosylation_events=occupied_glycosites,
hypothesis_name=name,
n_processes=processes)
try:
builder.start()
record = project_hypothesis.HypothesisRecordSet(database_connection)
hypothesis_record = None
for item in record:
if item.uuid == builder.hypothesis.uuid:
hypothesis_record = item
hypothesis_record = hypothesis_record._replace(
user_id=channel.user.id)
channel.send(
Message(hypothesis_record.to_json(), "new-hypothesis"))
break
else:
channel.send(
Message("Something went wrong (%r)" % (list(record), )))
except Exception:
channel.send(Message.traceback())