def __init__(self):
"""
Initialize a CodingBlockGraph
"""
# Initialize from PacbpCollectionGraph
PacbpCollectionGraph.__init__(self)
# short name tag for printing
self._short_name = "IWPCBG"
# some GLOBAL variables that are required in class functions
#self.ALTERNATIVE_ALIGNMENT_OVERLAP_RATIO = alternative_alignment_overlap_ratio
# 08/04/09 smallest omsr size must be 3 (means 4 AAs overall aligned)
# this is defined in settings.codingblockgraph
#self.MINIMAL_OVERAL_SPANNING_RANGE_SIZE = minimal_overal_spanning_range_size
# attribute needed to set the GeneTreeGraph into
#self._GENETREE = None
# attributes to cache OMSR and related data structures
self._omsr = {} # Overall Minimal Spanning Range
self._msr = {} # Minimal Spanning Range
self._maxsr = {} # MAXimal Spanning Range
def __init__(
self,
alternative_alignment_overlap_ratio=ALTERNATIVE_ALIGNMENT_OVERLAP_RATIO
):
"""
Initialize a LowSimilarityRegionCodingBlockGraph
"""
# Initialize from PacbpCollectionGraph, NOT from CodingBlockGraph
PacbpCollectionGraph.__init__(self)
self._node_object = {} # in use for orf objects
self.pacbps = {} # optional, not required
# N.B. key of pacbps is different as
# in CodingBlockGraph.
# NOT: (pacb_identifier, node1, node2)
# BUT: (node1, node2)
# short name tag for printing
self._short_name = "lsrCBG"
# set special attributes needed
self._splicedonorgraph = None
self._spliceacceptorgraph = None
self._stopcodongraph = None
self._startcodongraph = None
# dicts for data of VISTA like tracks
self._paoc_per_organism = {} # attribute stays EMPTY!!
self._pasc_per_organism = {} # attribute stays EMPTY!!
# attribute needed to set the GeneTreeGraph into
self._GENETREE = None
# attribute for cexpanderanalyses data
self._cexpander = None
# attributes that are needed once added into a genestructure
self.IS_FIRST = False
self.IS_LAST = False
self.IS_IGNORED = False
self.IS_SPLITTED = True # this class is always IS_SPLITTED
self.IS_5P_SPLITTED = True # this class is always IS_SPLITTED
self.IS_3P_SPLITTED = True # this class is always IS_SPLITTED
# set LowSimilarityRegion specific attributes
self._omsr = {}
self._forced_3p_ends = {}
self._forced_5p_ends = {}
def has_edge(self,u,v):
""" OVERRIDES GraphPlus.has_edge() """
if len(self.nodes) == 2 and ( self.weights.keys() == [(u,v),(v,u)] or self.weights.keys() == [(v,u),(u,v)] ):
# hmm.... escape. Weights are okay, nut nodes not.
# Temporarily allow this; it can happen in InwardsPointingCodingblockGraphs
return True
else:
return PacbpCollectionGraph.has_edge(self,u,v)
def CodingBlockGraph2PacbpCollectionGraph(cbg):
"""
Convert CodingBlockGraph 2 PacbpCollectionGraph -> a backwards conversion!
@attention: function just converts, error check is not performed here!
@type cbg: CodingBlockGraph
@param cbg: CodingBlockGraph instance
@rtype: PacbpCollectionGraph
@return: PacbpCollectionGraph instance
"""
from graph_pacbpcollection import PacbpCollectionGraph
pcg = PacbpCollectionGraph()
pcg.nodes = deepcopy(cbg.nodes)
pcg.weights = deepcopy(cbg.weights)
pcg.pacbps = deepcopy(cbg.pacbps)
return pcg
def CodingBlockGraph2PacbpCollectionGraph(cbg):
"""
Convert CodingBlockGraph 2 PacbpCollectionGraph -> a backwards conversion!
@attention: function just converts, error check is not performed here!
@type cbg: CodingBlockGraph
@param cbg: CodingBlockGraph instance
@rtype: PacbpCollectionGraph
@return: PacbpCollectionGraph instance
"""
from graph_pacbpcollection import PacbpCollectionGraph
pcg = PacbpCollectionGraph()
pcg.nodes = deepcopy(cbg.nodes)
pcg.weights = deepcopy(cbg.weights)
pcg.pacbps = deepcopy(cbg.pacbps)
return pcg
def __init__(self,alternative_alignment_overlap_ratio=ALTERNATIVE_ALIGNMENT_OVERLAP_RATIO):
"""
Initialize a LowSimilarityRegionCodingBlockGraph
"""
# Initialize from PacbpCollectionGraph, NOT from CodingBlockGraph
PacbpCollectionGraph.__init__(self)
self._node_object = {} # in use for orf objects
self.pacbps = {} # optional, not required
# N.B. key of pacbps is different as
# in CodingBlockGraph.
# NOT: (pacb_identifier, node1, node2)
# BUT: (node1, node2)
# short name tag for printing
self._short_name = "lsrCBG"
# set special attributes needed
self._splicedonorgraph = None
self._spliceacceptorgraph = None
self._stopcodongraph = None
self._startcodongraph = None
# dicts for data of VISTA like tracks
self._paoc_per_organism = {} # attribute stays EMPTY!!
self._pasc_per_organism = {} # attribute stays EMPTY!!
# attribute needed to set the GeneTreeGraph into
self._GENETREE = None
# attribute for cexpanderanalyses data
self._cexpander = None
# attributes that are needed once added into a genestructure
self.IS_FIRST = False
self.IS_LAST = False
self.IS_IGNORED = False
self.IS_SPLITTED = True # this class is always IS_SPLITTED
self.IS_5P_SPLITTED = True # this class is always IS_SPLITTED
self.IS_3P_SPLITTED = True # this class is always IS_SPLITTED
# set LowSimilarityRegion specific attributes
self._omsr = {}
self._forced_3p_ends = {}
self._forced_5p_ends = {}
def has_edge(self, u, v):
""" OVERRIDES GraphPlus.has_edge() """
if len(self.nodes) == 2 and (self.weights.keys() == [(u, v), (v, u)]
or self.weights.keys() == [(v, u),
(u, v)]):
# hmm.... escape. Weights are okay, nut nodes not.
# Temporarily allow this; it can happen in InwardsPointingCodingblockGraphs
return True
else:
return PacbpCollectionGraph.has_edge(self, u, v)
def __init__(self):
"""
Initialize a CodingBlockGraph
"""
# Initialize from PacbpCollectionGraph
PacbpCollectionGraph.__init__(self)
# short name tag for printing
self._short_name = "IWPCBG"
# some GLOBAL variables that are required in class functions
#self.ALTERNATIVE_ALIGNMENT_OVERLAP_RATIO = alternative_alignment_overlap_ratio
# 08/04/09 smallest omsr size must be 3 (means 4 AAs overall aligned)
# this is defined in settings.codingblockgraph
#self.MINIMAL_OVERAL_SPANNING_RANGE_SIZE = minimal_overal_spanning_range_size
# attribute needed to set the GeneTreeGraph into
#self._GENETREE = None
# attributes to cache OMSR and related data structures
self._omsr = {} # Overall Minimal Spanning Range
self._msr = {} # Minimal Spanning Range
self._maxsr = {} # MAXimal Spanning Range
