def _is_intermediate_overlapping_cbg_a_gsg_scaffold_enrichment(gsg,
cbgA,cbgB,cbgC,minimal_scaffold_aa_enrichment=5):
"""
"""
if not (gsg and cbgA and cbgB and cbgC):
# (most likely) cbgA or cbgC is not defined
# function behavious should be ti return False
return False
if not cbgA.mutual_nodes(cbgC):
# series of CBGs does not represent an suitable
# gene structure scaffold -> return False
return False
# perform this check
from graph_genestructure import GenestructureOfCodingBlockGraphs
partGSG = GenestructureOfCodingBlockGraphs(gsg.input)
partGSG.codingblockgraphs = [ cbgA,cbgB,cbgC ]
partGSG._GENETREE = gsg._GENETREE
partOMSRa = partGSG.overall_minimal_spanning_range()
partGSG.codingblockgraphs = [ cbgA,cbgC ]
partOMSRb = partGSG.overall_minimal_spanning_range()
scaffold_enrichments = []
for node in cbgA.mutual_nodes(cbgC):
org = gsg.organism_by_node(node)
scaffold_enrichments.append(
len(partOMSRa[org]) - len(partOMSRb[org]) >=\
minimal_scaffold_aa_enrichment
)
# check if True in scaffold_enrichments
if True in scaffold_enrichments:
return True
else:
return False
def replace_scaffold_breaking_cbgs(self,verbose=False):
"""
(Try) to replace CBG that break the GSG scaffold by other CBGs
@type verbose: Boolean
@param verbose: print status/debugging messages to STDOUT
@rtype: Boolean
@return: Is any CBG replaced?
"""
# Boolean return value
scaffold_breaking_cbg_replaced = False
for cbgpos in self.cbgpositerator(reversed=True)[1:]:
cbg = self.codingblockgraphs[cbgpos]
if cbg.__class__.__name__ == 'LowSimilarityRegionCodingBlockGraph':
continue
if cbg.node_count() < self.EXACT_SG_NODE_COUNT:
continue
# loop forwards through the GSG and look for mutual nodes
identical_nodes = []
for backwardspos in range(cbgpos+1,len(self)):
comparecbg = self.codingblockgraphs[backwardspos]
if cbg.mutual_nodes(comparecbg):
identical_nodes.append(True)
break
else:
identical_nodes.append(False)
if not identical_nodes:
continue # final CBG -> continue
elif identical_nodes == [True]:
continue # neighboring node has mutual nodes -> continue
elif identical_nodes.count(True) == 0:
continue # no mutual nodes at all -> continue
else:
# this is what we are looking for, a list like
# [ False, ... True ] with >1 False
# get total_weights of the intermediate CBGs
tws = [ self.codingblockgraphs[_pos].total_weight() for\
_pos in range(cbgpos+1,backwardspos) ]
################################################################
if verbose:
print cbgpos, backwardspos, identical_nodes
print cbg
print tws
print comparecbg
################################################################
# first, check if the CBGs are already partially overlapping
# if so, get rid of this intermediate CBG
omsrdist = cbg.omsr_distance_between_codingblocks(comparecbg)
if max(omsrdist.values()) <= 1:
# yes, all organisms glue these CBGs perfectly together
# just remove this one without further checks
cbg._CBGinterface3p = None
comparecbg._CBGinterface5p = None
self.codingblockgraphs.__setslice__(
cbgpos+1,
backwardspos+1,
[ comparecbg ] )
scaffold_breaking_cbg_replaced = True
# go to the next cbg in the list
continue
# do a more eleborate check by trying to create a CBG
# in this large_scaffold_gap
from graph_genestructure import GenestructureOfCodingBlockGraphs
partialGSG = GenestructureOfCodingBlockGraphs(self.input)
partialGSG.codingblockgraphs = [ cbg, comparecbg ]
partialGSG._GENETREE = self._GENETREE
partialGSG.create_large_intermediate_cbg_for_scaffold_gap(
sprdif_min_node_count = 2,
cbg_min_node_count = self.EXACT_SG_NODE_COUNT,
verbose = verbose
)
if len(partialGSG) == 2:
############################################################
if verbose: print "NO scaffold CBGs found!"
############################################################
pass
else:
new_tws = [ _cbg.total_weight() for _cbg in\
partialGSG.codingblockgraphs[1:-1] ]
if sum(new_tws) > sum(tws):
# replace!
self.codingblockgraphs.__setslice__(
cbgpos+1,
backwardspos,
partialGSG.codingblockgraphs[1:-1] )
scaffold_breaking_cbg_replaced = True
else:
pass
############################################################
if verbose:
if sum(new_tws) > sum(tws):
print "REPLACING scaffold-breaking CBGs!!!"
else:
print "MAINTAINING scaffold-breaking CBGs!!!"
for cbg in partialGSG: print cbg
############################################################
# return if CBGs are removed
return scaffold_breaking_cbg_replaced
