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()