def PacbpCollectionGraph2CodingBlockGraph(pcg):
"""
Convert PacbpCollectionGraph 2 CodingBlockGraph
@attention: function just converts, error check is not performed here!
@type pcg: PacbpCollectionGraph
@param pcg: PacbpCollectionGraph instance
@rtype: CodingBlockGraph
@return: CodingBlockGraph instance
"""
from graph_codingblock import CodingBlockGraph
cbg = CodingBlockGraph()
cbg.nodes = pcg.nodes
cbg.weights = pcg.weights
cbg.pacbps = pcg.pacbps
return cbg
def PacbpCollectionGraph2CodingBlockGraph(pcg):
"""
Convert PacbpCollectionGraph 2 CodingBlockGraph
@attention: function just converts, error check is not performed here!
@type pcg: PacbpCollectionGraph
@param pcg: PacbpCollectionGraph instance
@rtype: CodingBlockGraph
@return: CodingBlockGraph instance
"""
from graph_codingblock import CodingBlockGraph
cbg = CodingBlockGraph()
cbg.nodes = pcg.nodes
cbg.weights = pcg.weights
cbg.pacbps = pcg.pacbps
return cbg
def ExonCollectionGraph2CodingBlockGraph(gra,is_first=False,is_last=False,firstCBG=None,lastCBG=None):
"""
Convert ECG -> CodingBlockGraph
@type gra: ExonCollectionGraph
@param gra: ExonCollectionGraph instance
@type is_first: Boolean
@param is_first: True or False (default False)
@type is_last: Boolean
@param is_last: True or False (default False)
@type firstCBG: CodingBlockGraph (or None)
@param firstCBG: ...
@type lastCBG: CodingBlockGraph (or None)
@param lastCBG: ...
@attention: make shure to specify arguments correctly!
@rtype: CodingBlockGraph
@return: CodingBlockGraph instance or None when failed!
"""
from graph_codingblock import CodingBlockGraph
cbg = CodingBlockGraph()
cbg.MINIMAL_OVERAL_SPANNING_RANGE_SIZE = 1
for ecgnode in gra.get_nodes():
cbg.add_node( gra.ecgnode2cbgnode(ecgnode) )
# make Pacbp objects for the edges if not done yet
if not gra.pacbps or len(gra.pacbps) != gra.edge_count():
gra.make_pacbps_for_edges()
# check if number of pacbps matches number of edges
if len(gra.pacbps) != gra.edge_count():
# pacbp creation failed for at least 1 edge -> no CBG!
return None
# check if connectivitysaturation == 1.0:
if gra.connectivitysaturation() != 1.0:
# no edge listed between some of the nodes!
return None
# transfer pacbps and edges to new CBG
for (key,ecgnode1,ecgnode2), pacbporf in gra.pacbps.iteritems():
# convert ECGnode to CBGnode
cbg_node1 = gra.ecgnode2cbgnode(ecgnode1)
cbg_node2 = gra.ecgnode2cbgnode(ecgnode2)
bitscore = key[0]
cbg.add_edge(cbg_node1,cbg_node2,wt=bitscore)
cbg.pacbps[(key,cbg_node1,cbg_node2)] = pacbporf
# fix pacbps that are already present in what is currently
# the first CBG. This is the case for nodes (exons) in the firstExonGraph
# that end with a CodingBlockEnd.
if firstCBG:
replacements = {}
for (key,node1,node2), pacbporf in cbg.pacbps.iteritems():
if firstCBG.has_edge(node1,node2):
startPos = pacbporf._get_original_alignment_pos_start()
firstpacbporf = firstCBG.get_pacbps_by_nodes(node1=node1,node2=node2)[0]
firstStartPos = firstpacbporf._get_original_alignment_pos_start()
if firstStartPos.query_pos <= startPos.query_pos and firstStartPos.sbjct_pos <= startPos.sbjct_pos:
replacements[(key,node1,node2)] = firstpacbporf
if replacements:
for (key,node1,node2), pacbporf in replacements.iteritems():
del( cbg.pacbps[(key,node1,node2)] )
newkey = pacbporf.construct_unique_key(node1,node2)
cbg.pacbps[(newkey,node1,node2)] = pacbporf
if lastCBG:
replacements = {}
for (key,node1,node2), pacbporf in cbg.pacbps.iteritems():
if lastCBG.has_edge(node1,node2):
endPos = pacbporf._get_original_alignment_pos_end()
lastpacbporf = lastCBG.get_pacbps_by_nodes(node1=node1,node2=node2)[0]
lastEndPos = lastpacbporf._get_original_alignment_pos_end()
if lastEndPos.query_pos >= endPos.query_pos and lastEndPos.sbjct_pos <= endPos.sbjct_pos:
replacements[(key,node1,node2)] = lastpacbporf
if replacements:
for (key,node1,node2), pacbporf in replacements.iteritems():
del( cbg.pacbps[(key,node1,node2)] )
newkey = pacbporf.construct_unique_key(node1,node2)
cbg.pacbps[(newkey,node1,node2)] = pacbporf
# Now make shure this CodingBlockGraph is fully compatible in the Genestructure
# That means, do some site scanning because this newcbg is inserted AFTER
# all the sitescanning has been done!
if not cbg.has_overall_minimal_spanning_range():
### print "ecg2cbg:", cbg, cbg.edge_count(), len(cbg.pacbps)
return None
# set the footprint of where this CBG came from
# this can be deleted lateron, but is not required per se
# this footprint is needed because the surrounding CBGs
# must get some (additional) forced splice sites that depend
# on the sites in the ExonCollectionGraph
cbg._ExonCollectionGraph = gra
# DO NOT update edge weights!!
# this wipes out the alignment evidence outside of the OMSR region
#cbg.update_edge_weights_by_minimal_spanning_range()
# make AlignedStopCodonGraph
cbg.align_stop_codons()
# create splicedonorgraph & align sites
cbg._splicedonorgraph = ExonCollectionGraph2DonorSiteCollectionGraph(gra)
cbg._splicedonorgraph.collection2alignedsites(
edges=gra.node_count()-1,
minimal_edges=gra.node_count()-1
)
if is_first:
# create tssgraph & align sites
dummyTSScolgra = ExonCollectionGraph2TranslationalStartSiteCollectionGraph(gra)
dummyTSScolgra.collection2alignedsites( edges=gra.node_count()-1 )
# make the *TRUE* TSScolgra and align them
cbg.harvest_elegiable_tss_sites()
cbg._startcodongraph.collection2alignedsites()
# place the dummyTSScolgra in front of the que
cbg._startcodongraph.alignedsites.insert( 0, dummyTSScolgra.alignedsites[0] )
# and assign _codingblockgraph attribute to all alignedsites;
# this is needed to do an is_optimal() check
for _algtss in cbg._startcodongraph.alignedsites:
_algtss._codingblockgraph = cbg
else:
# create spliceacceptorgraph & align sites
cbg._spliceacceptorgraph = ExonCollectionGraph2AcceptorSiteCollectionGraph(gra)
cbg._spliceacceptorgraph.collection2alignedsites(
edges=gra.node_count()-1,
minimal_edges=gra.node_count()-1
)
if is_first:
# make SpliceSiteCollectionGraphs
### print "ecg2cbg:(1)", cbg
cbg.harvest_elegiable_acceptor_sites(projected_acceptors={},forced_codingblock_ends={},prev=None)
# do site alignment of acceptors
cbg._spliceacceptorgraph.collection2alignedsites(edges=cbg.node_count()-1,minimal_edges=2)
if is_last:
# make SpliceSiteCollectionGraphs
cbg.harvest_elegiable_donor_sites(projected_donors={},forced_codingblock_ends={},next=None)
# do site alignment of acceptors
cbg._splicedonorgraph.collection2alignedsites(edges=cbg.node_count()-1,minimal_edges=2)
# done! return the CBG
### print "ecg2cbg:done!", cbg
return cbg
