def __init__(self, mzid_path, connection, hypothesis_id, include_baseline_peptides=True,
target_proteins=None, reference_fasta=None, peptide_length_range=(5, 60)):
DatabaseBoundOperation.__init__(self, connection)
MzIdentMLProteomeExtraction.__init__(self, mzid_path, reference_fasta)
self.hypothesis_id = hypothesis_id
self.target_proteins = target_proteins
self.include_baseline_peptides = include_baseline_peptides
self.peptide_length_range = peptide_length_range or (5, 60)
def __init__(self, connection, hypothesis_id=None, *args, **kwargs):
if hypothesis_id is None:
hypothesis_id = 1
DatabaseBoundOperation.__init__(self, connection)
PeptideCollectionBase.__init__(self, *args, **kwargs)
self.hypothesis_id = hypothesis_id
self._operation_count = 0
self._batch_size = int(kwargs.get("batch_size", 1000))
def __init__(self, database_connection, hypothesis_name=None, glycan_hypothesis_id=None, full_cross_product=True):
DatabaseBoundOperation.__init__(self, database_connection)
self._hypothesis_name = hypothesis_name
self._hypothesis_id = None
self._hypothesis = None
self._glycan_hypothesis_id = glycan_hypothesis_id
self.uuid = str(uuid4().hex)
self.total_glycan_combination_count = -1
self.full_cross_product = full_cross_product
def __init__(self, database_connection):
DatabaseBoundOperation.__init__(self, database_connection)
self.hypothesis_id = None
self.glycan_hypothesis_id = None
self._glycan_hypothesis_migrator = None
self.protein_id_map = dict()
self.peptide_id_map = dict()
self.glycan_combination_id_map = dict()
self.glycopeptide_id_map = dict()
def __init__(self, database_connection, hypothesis_name=None, uuid=None):
if uuid is None:
uuid = str(uuid4().hex)
DatabaseBoundOperation.__init__(self, database_connection)
self._hypothesis_name = hypothesis_name
self._hypothesis_id = None
self._hypothesis = None
self._structure_class_loader = None
self.uuid = uuid
def __init__(self, connection, analysis_name, sample_run, chromatogram_extractor):
DatabaseBoundOperation.__init__(self, connection)
self.sample_run = sample_run
self.chromatogram_extractor = chromatogram_extractor
self._seed_analysis_name = analysis_name
self._analysis_serializer = None
self._sample_migrator = None
def __init__(self, connection, hypothesis_id, target_proteins=None,
constant_modifications=None, variable_modifications=None):
if constant_modifications is None:
constant_modifications = []
if variable_modifications is None:
variable_modifications = []
DatabaseBoundOperation.__init__(self, connection)
self.hypothesis_id = hypothesis_id
self.target_proteins = target_proteins
self.constant_modifications = constant_modifications
self.variable_modifications = variable_modifications
def __init__(self, connection, hypothesis_id=1, cache_size=DEFAULT_CACHE_SIZE,
loading_interval=DEFAULT_LOADING_INTERVAL,
threshold_cache_total_count=DEFAULT_THRESHOLD_CACHE_TOTAL_COUNT,
model_type=Glycopeptide):
DatabaseBoundOperation.__init__(self, connection)
self.hypothesis_id = hypothesis_id
self.model_type = model_type
self.loading_interval = loading_interval
self.threshold_cache_total_count = threshold_cache_total_count
self._intervals = LRUIntervalSet([], cache_size)
self._ignored_intervals = IntervalSet([])
self.proteins = ProteinIndex(self.session, self.hypothesis_id)
self.peptides = PeptideIndex(self.session, self.hypothesis_id)
def __init__(self, database_connection, analysis_id, output_path, mzml_path=None):
DatabaseBoundOperation.__init__(self, database_connection)
self.analysis_id = analysis_id
self.mzml_path = mzml_path
self.output_path = output_path
self.analysis = self.session.query(serialize.Analysis).get(self.analysis_id)
self.scan_loader = None
self._mpl_style = {
'figure.facecolor': 'white',
'figure.edgecolor': 'white',
'font.size': 10,
'savefig.dpi': 72,
'figure.subplot.bottom': .125
}
def __init__(self,
connection,
hypothesis_id,
target_proteins=None,
constant_modifications=None,
variable_modifications=None):
if constant_modifications is None:
constant_modifications = []
if variable_modifications is None:
variable_modifications = []
DatabaseBoundOperation.__init__(self, connection)
self.hypothesis_id = hypothesis_id
self.target_proteins = target_proteins
self.constant_modifications = constant_modifications
self.variable_modifications = variable_modifications
def __init__(
self,
connection,
hypothesis_id=1,
cache_size=DEFAULT_CACHE_SIZE,
loading_interval=DEFAULT_LOADING_INTERVAL,
threshold_cache_total_count=DEFAULT_THRESHOLD_CACHE_TOTAL_COUNT,
model_type=Glycopeptide):
DatabaseBoundOperation.__init__(self, connection)
self.hypothesis_id = hypothesis_id
self.model_type = model_type
self.loading_interval = loading_interval
self.threshold_cache_total_count = threshold_cache_total_count
self._intervals = LRUIntervalSet([], cache_size)
self._ignored_intervals = IntervalSet([])
self.proteins = ProteinIndex(self.session, self.hypothesis_id)
self.peptides = PeptideIndex(self.session, self.hypothesis_id)
def __init__(self, connection, source_hypothesis_id, target_hypothesis_id, max_size=1):
DatabaseBoundOperation.__init__(self, connection)
self.source_hypothesis_id = source_hypothesis_id
self.target_hypothesis_id = target_hypothesis_id
self.max_size = max_size
self.total_count = 0
def __init__(self, connection, hypothesis_id):
DatabaseBoundOperation.__init__(self, connection)
self.hypothesis_id = hypothesis_id
self.index = PeptideIndex()
self.index.populate(self._get_all_peptides())
def __init__(self, database_connection, source, source_type, source_identifier=None):
DatabaseBoundOperation.__init__(self, database_connection)
self.source = source
self.source_type = source_type
self.source_identifier = source_identifier
def __init__(self, connection, hypothesis_id):
DatabaseBoundOperation.__init__(self, connection)
self.hypothesis_id = hypothesis_id
self.index = PeptideIndex()
self.index.populate(self._get_all_peptides())
def __init__(self, database_connection, hypothesis_id):
DatabaseBoundOperation.__init__(self, database_connection)
self.hypothesis_id = hypothesis_id
def __init__(self, connection):
DatabaseBoundOperation.__init__(self, connection)
self.sample_run_id = None
self.ms_scan_id_map = dict()
self.peak_id_map = dict()
def __init__(self, database_connection):
DatabaseBoundOperation.__init__(self, database_connection)
self.hypothesis_id = None
self.glycan_composition_id_map = dict()
self._structure_class_loader = None
def __init__(self, connection, hypothesis_id):
DatabaseBoundOperation.__init__(self, connection)
self.hypothesis_id = hypothesis_id
def __init__(self, connection):
DatabaseBoundOperation.__init__(self, connection)
self.sample_run_id = None
self.ms_scan_id_map = dict()
self.peak_id_map = dict()