def add_codingblocks(self,
cbglist,
log_debug=False,
max_cbg_gtg_topo_dif=None,
max_cbg_gtg_abs_dif=None,
min_cbg_gtg_id_ratio=None,
omit_conditional_addition=False,
min_tcode_omsr=None):
"""
(Try to) add multiple CodingBlockGraphs to the genestructure
@type cbglist: list
@param cbglist: list of CodingBlockGraph objects to be added to the genestructure
@type max_cbg_gtg_topo_dif: float (or None)
@param max_cbg_gtg_topo_dif:
@type max_cbg_gtg_abs_dif: float (or None)
@param max_cbg_gtg_abs_dif:
@type max_cbg_gtg_id_ratio: float (or None)
@param max_cbg_gtg_id_ratio:
@type min_tcode_omsr: float (or None)
@param min_tcode_omsr:
@type omit_conditional_addition: Boolean
@param omit_conditional_addition: omit all CBG quality checks; just
verify if the CBG is placeable based on the OMSR coordinates
@rtype: Boolean
@return: True or False, weather or not at least 1 CodingBlockGraph was added
"""
# add cbg's after ordering on total weight
statusses = []
# update edge weights to minimal spanning range
for sg in cbglist:
sg.update_edge_weights_by_minimal_spanning_range()
for cbg in ordering.order_cbgraphlist(cbglist):
status = self.add_codingblock(
cbg,
log_debug=log_debug,
max_cbg_gtg_topo_dif=max_cbg_gtg_topo_dif,
max_cbg_gtg_abs_dif=max_cbg_gtg_abs_dif,
min_cbg_gtg_id_ratio=min_cbg_gtg_id_ratio,
min_tcode_omsr=min_tcode_omsr,
omit_conditional_addition=omit_conditional_addition,
)
statusses.append(status)
if True in statusses:
return True
else:
return False
def add_codingblocks(self,cbglist,log_debug=False,
max_cbg_gtg_topo_dif=None,
max_cbg_gtg_abs_dif=None,
min_cbg_gtg_id_ratio=None,
omit_conditional_addition=False,
min_tcode_omsr=None ):
"""
(Try to) add multiple CodingBlockGraphs to the genestructure
@type cbglist: list
@param cbglist: list of CodingBlockGraph objects to be added to the genestructure
@type max_cbg_gtg_topo_dif: float (or None)
@param max_cbg_gtg_topo_dif:
@type max_cbg_gtg_abs_dif: float (or None)
@param max_cbg_gtg_abs_dif:
@type max_cbg_gtg_id_ratio: float (or None)
@param max_cbg_gtg_id_ratio:
@type min_tcode_omsr: float (or None)
@param min_tcode_omsr:
@type omit_conditional_addition: Boolean
@param omit_conditional_addition: omit all CBG quality checks; just
verify if the CBG is placeable based on the OMSR coordinates
@rtype: Boolean
@return: True or False, weather or not at least 1 CodingBlockGraph was added
"""
# add cbg's after ordering on total weight
statusses = []
# update edge weights to minimal spanning range
for sg in cbglist:
sg.update_edge_weights_by_minimal_spanning_range()
for cbg in ordering.order_cbgraphlist(cbglist):
status = self.add_codingblock(cbg,log_debug=log_debug,
max_cbg_gtg_topo_dif=max_cbg_gtg_topo_dif,
max_cbg_gtg_abs_dif=max_cbg_gtg_abs_dif,
min_cbg_gtg_id_ratio=min_cbg_gtg_id_ratio,
min_tcode_omsr=min_tcode_omsr,
omit_conditional_addition=omit_conditional_addition,
)
statusses.append( status )
if True in statusses:
return True
else:
return False
def findmostlikelyCBG2GSGinsert(partialGSG,
cbglist,
order_cbgs_by_total_weight=True,
reorder_cbgs_on_node_occurrence=True,
optimizetinyexoninterface=True,
verbose=False):
"""
"""
# if no CBG in list -> done!
if not cbglist: return partialGSG
# make interfaces in the partialGSG
created = partialGSG.create_cbginterfaces()
gsgsize = len(partialGSG)
if order_cbgs_by_total_weight:
# order graphs by total weight
cbglist = ordering.order_cbgraphlist(cbglist)
if reorder_cbgs_on_node_occurrence:
# get prev and next cbg from partialGSG
if len(partialGSG) >= 2:
prev = partialGSG.codingblockgraphs[0]
next = partialGSG.codingblockgraphs[-1]
elif len(partialGSG) == 1:
prev, next = None, partialGSG.codingblockgraphs[0]
else:
prev, next = None, None
# re-order on node occurrence.
cbglist = ordering.reorder_cbgs_on_node_occurrence(cbglist,
prev=prev,
next=next)
####################################################################
if verbose and partialGSG and cbglist:
print "elegiable CBGs for addition in partialGSG"
for cbg in cbglist:
print cbg
####################################################################
# now try to insert CBGs in the partialGSG
# we try several insertions, starting with the most stringest one
############################################################
# (1) only do both options for the top listed CBG ####
# perfect cbgIF(s), topologically sound CBGs ####
# perfect cbgIF(s), CBG2GTG topology not tested ####
############################################################
is_added = _place_cbg_in_partialgsg(
[cbglist[0]],
partialGSG,
omit_conditional_addition=False,
optimizetinyexoninterface=optimizetinyexoninterface,
verbose=verbose)
is_added = _place_cbg_in_partialgsg(
[cbglist[0]],
partialGSG,
omit_conditional_addition=True,
optimizetinyexoninterface=optimizetinyexoninterface,
verbose=verbose)
############################################################
# (2) perfect cbgIF(s), topologically sound CBGs ####
############################################################
is_added = _place_cbg_in_partialgsg(
cbglist,
partialGSG,
omit_conditional_addition=False,
optimizetinyexoninterface=optimizetinyexoninterface,
verbose=verbose)
############################################################
# (3) perfect cbgIF(s), CBG2GTG topology not tested ####
############################################################
is_added = _place_cbg_in_partialgsg(
cbglist,
partialGSG,
omit_conditional_addition=True,
optimizetinyexoninterface=optimizetinyexoninterface,
verbose=verbose)
# when partialGSG is not enlarged, its cbgIFs are likely
# distorted in the proces of trying novel CBG inserts.
# Recreate the cbgIFs here
if len(partialGSG) == gsgsize:
if gsgsize >= 2:
partialGSG.clear_central_cbginterfaces()
partialGSG.create_cbginterfaces()
if gsgsize == 2:
# most obvious case of 2 CBGs in the GSG
partialGSG.codingblockgraphs[0].IS_3P_SPLITTED = False
partialGSG.codingblockgraphs[1].IS_5P_SPLITTED = False
if not partialGSG.codingblockgraphs[0].IS_5P_SPLITTED:
partialGSG.codingblockgraphs[0].IS_SPLITTED = False
if not partialGSG.codingblockgraphs[1].IS_3P_SPLITTED:
partialGSG.codingblockgraphs[1].IS_SPLITTED = False
else:
# a partialGSG of only a single CBG (first or last CBG)
partialGSG.codingblockgraphs[0]._CBGinterface5p = None
partialGSG.codingblockgraphs[0]._CBGinterface3p = None
# Done with this function. Return the (incremented) partialGSG
return partialGSG
def findmostlikelyCBG2GSGinsert(partialGSG,cbglist,
order_cbgs_by_total_weight=True,
reorder_cbgs_on_node_occurrence=True,
optimizetinyexoninterface=True,
verbose=False):
"""
"""
# if no CBG in list -> done!
if not cbglist: return partialGSG
# make interfaces in the partialGSG
created = partialGSG.create_cbginterfaces()
gsgsize = len(partialGSG)
if order_cbgs_by_total_weight:
# order graphs by total weight
cbglist = ordering.order_cbgraphlist(cbglist)
if reorder_cbgs_on_node_occurrence:
# get prev and next cbg from partialGSG
if len(partialGSG) >= 2:
prev = partialGSG.codingblockgraphs[0]
next = partialGSG.codingblockgraphs[-1]
elif len(partialGSG) == 1:
prev, next = None, partialGSG.codingblockgraphs[0]
else:
prev, next = None, None
# re-order on node occurrence.
cbglist = ordering.reorder_cbgs_on_node_occurrence(cbglist,prev=prev,next=next)
####################################################################
if verbose and partialGSG and cbglist:
print "elegiable CBGs for addition in partialGSG"
for cbg in cbglist: print cbg
####################################################################
# now try to insert CBGs in the partialGSG
# we try several insertions, starting with the most stringest one
############################################################
# (1) only do both options for the top listed CBG ####
# perfect cbgIF(s), topologically sound CBGs ####
# perfect cbgIF(s), CBG2GTG topology not tested ####
############################################################
is_added = _place_cbg_in_partialgsg([ cbglist[0] ],partialGSG,
omit_conditional_addition=False,
optimizetinyexoninterface=optimizetinyexoninterface,
verbose=verbose )
is_added = _place_cbg_in_partialgsg([ cbglist[0] ],partialGSG,
omit_conditional_addition=True,
optimizetinyexoninterface=optimizetinyexoninterface,
verbose=verbose )
############################################################
# (2) perfect cbgIF(s), topologically sound CBGs ####
############################################################
is_added = _place_cbg_in_partialgsg(cbglist,partialGSG,
omit_conditional_addition=False,
optimizetinyexoninterface=optimizetinyexoninterface,
verbose=verbose )
############################################################
# (3) perfect cbgIF(s), CBG2GTG topology not tested ####
############################################################
is_added = _place_cbg_in_partialgsg(cbglist,partialGSG,
omit_conditional_addition=True,
optimizetinyexoninterface=optimizetinyexoninterface,
verbose=verbose )
# when partialGSG is not enlarged, its cbgIFs are likely
# distorted in the proces of trying novel CBG inserts.
# Recreate the cbgIFs here
if len(partialGSG) == gsgsize:
if gsgsize >=2:
partialGSG.clear_central_cbginterfaces()
partialGSG.create_cbginterfaces()
if gsgsize == 2:
# most obvious case of 2 CBGs in the GSG
partialGSG.codingblockgraphs[0].IS_3P_SPLITTED = False
partialGSG.codingblockgraphs[1].IS_5P_SPLITTED = False
if not partialGSG.codingblockgraphs[0].IS_5P_SPLITTED:
partialGSG.codingblockgraphs[0].IS_SPLITTED = False
if not partialGSG.codingblockgraphs[1].IS_3P_SPLITTED:
partialGSG.codingblockgraphs[1].IS_SPLITTED = False
else:
# a partialGSG of only a single CBG (first or last CBG)
partialGSG.codingblockgraphs[0]._CBGinterface5p = None
partialGSG.codingblockgraphs[0]._CBGinterface3p = None
# Done with this function. Return the (incremented) partialGSG
return partialGSG
