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)