def __init__(self,max_node_count=None,min_pssm_score=None,aligned_site_aa_offset=None,tcode_5p_windowsize=TCODE_TSS_5P_WINDOW,tcode_3p_windowsize=TCODE_TSS_3P_WINDOW): """ Initialize asa BasalAlignedPssmObjectGraph, then extend """ BasalAlignedPssmObjectGraph.__init__(self,max_node_count=max_node_count, min_pssm_score=min_pssm_score, aligned_site_aa_offset=aligned_site_aa_offset ) # attributes for TCODE data self._tcode5pscore = {} self._tcode3pscore = {} self._TCODE_5P_WINDOWSIZE = tcode_5p_windowsize self._TCODE_3P_WINDOWSIZE = tcode_3p_windowsize # attribute for storing this CBG object # when not HARD-SET into this postion, # is_optimal_gtgweakestnode() will crash! self._codingblockgraph = None # is_optimal_xxx thresholds self._optimal_min_tcode = ALIGNEDTSSGRAPH_OPTIMALITY_MIN_TCODE self._optimal_max_tcode = ALIGNEDTSSGRAPH_OPTIMALITY_MAX_TCODE self._optimal_min_weight = ALIGNEDTSSGRAPH_OPTIMALITY_MIN_WEIGHT self._optimal_max_weight = ALIGNEDTSSGRAPH_OPTIMALITY_MAX_WEIGHT self._optimal_min_gtgweakest = ALIGNEDTSSGRAPH_OPTIMALITY_MIN_GTGWEAKEST self._optimal_max_gtgweakest = ALIGNEDTSSGRAPH_OPTIMALITY_MAX_GTGWEAKEST
def togff(self,gff={},organism=None): """ Create gff tuple for aligned splice site of a specific organism @attention: See AlignedPssmObjectGraph.togff, CAN BE OVERRIDDEN HERE IF DESIRED!! """ return BasalAlignedPssmObjectGraph.togff(self,organism=organism,gff=gff)
def cumulative_score(self): """ Cumulative score of a group of aligned TranslationalStartSites (TSS) @attention: See AlignedPssmObjectGraph.cumulative_score, CAN BE OVERRIDDEN HERE IF DESIRED!! """ return BasalAlignedPssmObjectGraph.cumulative_score(self)