def __init__(self,tcode_5p_windowsize=201,tcode_3p_windowsize=201): """ Initialize a AlignedStartCodonGraph """ OrganismGraph.__init__(self) self._tcode5pscore = {} self._tcode3pscore = {} self._TCODE_5P_WINDOWSIZE = tcode_5p_windowsize self._TCODE_3P_WINDOWSIZE = tcode_3p_windowsize
def __init__(self,max_node_count=None,min_pssm_score=None,aligned_site_aa_offset=None): """ Initialize a AlignedPssmObjectGraph """ OrganismGraph.__init__(self) self._node_pssm = {} self._node_object = {} self.MIN_PSSM_SCORE = min_pssm_score self.MAX_NODE_COUNT = max_node_count self.ALIGNED_SITE_AA_OFFSET = aligned_site_aa_offset
def __init__(self): """ Initialize a GeneTreeGraph """ # Initialize as an OrganismGraph OrganismGraph.__init__(self) # self.weights contains identityscores # add similar dicts for aa_identity, bitscore_ratios and nt_identity self._aa_identity_percentages = {} self._bitscore_ratios = {} self._nt_identity_percentages = {}
def __init__(self): """ Initialize a GeneTreeGraph """ # Initialize as an OrganismGraph OrganismGraph.__init__(self) # self.weights contains identityscores # add similar dicts for aa_identity, bitscore_ratios and nt_identity self._aa_identity_percentages = {} self._bitscore_ratios = {} self._nt_identity_percentages = {}
def __init__(self): """ Initialize a PacbpCollectionGraph """ # Initialize as an OrganismGraph OrganismGraph.__init__(self) # set extra attributes self._node_object = {} self._node_pssm = {} # needed for backwards compatibilty with PacbpCollectionGraph, CodingBlockGraph self.pacbps = {} self._omsr = {}
def __init__(self): """ Initialize a PssmObjectCollectionGraph; objects on orfs on pacbporfs (splice sites, start sites, stop sites) """ OrganismGraph.__init__(self) self._node_pssm = {} self._node_object = {} self.MIN_PSSM_SCORE = None # list to store aligned sites graphs self.alignedsites = [] # dictionary keeping track of considered range self._organism_consideredrange = {} # Attributes storing information for thresholds of # how this collection was generated self.ALIGNED_SITE_AA_OFFSET = None self.MIN_PSSM_SCORE = None
def __init__(self,cbg,tcode_5p_windowsize=201,tcode_3p_windowsize=201): """ Initialize a AlignedStopCodonGraph """ OrganismGraph.__init__(self) # attribute for storing the CBG itself self._codingblockgraph = cbg # attributes for TCODE data self._tcode5pscore = {} self._tcode3pscore = {} self._TCODE_5P_WINDOWSIZE = tcode_5p_windowsize self._TCODE_3P_WINDOWSIZE = tcode_3p_windowsize # is_optimal_xxx thresholds self._optimal_min_tcode = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_TCODE self._optimal_max_tcode = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_TCODE self._optimal_min_weight = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_WEIGHT self._optimal_max_weight = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_WEIGHT self._optimal_min_gtgweakest = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_GTGWEAKEST self._optimal_max_gtgweakest = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_GTGWEAKEST # run function codingblock_collectionharvesting.align_stop_codons # to fully initialize the object self = codingblock_collectionharvesting.align_stop_codons(cbg,self)
def __init__(self, cbg, tcode_5p_windowsize=201, tcode_3p_windowsize=201): """ Initialize a AlignedStopCodonGraph """ OrganismGraph.__init__(self) # attribute for storing the CBG itself self._codingblockgraph = cbg # attributes for TCODE data self._tcode5pscore = {} self._tcode3pscore = {} self._TCODE_5P_WINDOWSIZE = tcode_5p_windowsize self._TCODE_3P_WINDOWSIZE = tcode_3p_windowsize # is_optimal_xxx thresholds self._optimal_min_tcode = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_TCODE self._optimal_max_tcode = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_TCODE self._optimal_min_weight = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_WEIGHT self._optimal_max_weight = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_WEIGHT self._optimal_min_gtgweakest = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_GTGWEAKEST self._optimal_max_gtgweakest = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_GTGWEAKEST # run function codingblock_collectionharvesting.align_stop_codons # to fully initialize the object self = codingblock_collectionharvesting.align_stop_codons(cbg, self)