def create_pacbpcollectiongraph_from_crossdata(
crossdata,
increment_to_graph=None):
"""
Create (incremental) PacbpCollectionGraph from crossdata dict structure
@type crossdata: dict
@param crossdata: crossdata <dict data structure>
@type increment_to_graph: None or PacbpCollectionGraph
@param increment_to_graph: when applied, increment crossdata to applied PCG
@rtype g: PacbpCollectionGraph
@return g: PacbpCollectionGraph
"""
if increment_to_graph:
# add new nodes to existing graph
g = increment_to_graph
else:
# create a new blank graph
from graphAbgp import PacbpCollectionGraph
g = PacbpCollectionGraph()
for (orgA,orgB) in crossdata.keys():
keys = crossdata[(orgA,orgB)]['accepted_pacbs'].keys()
# sort keys in order to start with highest bitscore
keys.sort()
keys.reverse()
for key in keys:
(bitscore,lenght,pointerA,pointerB) = key
nodeA = (orgA,pointerA)
nodeB = (orgB,pointerB)
# check if (org,ORF) node exist already
if nodeA not in g.get_nodes(): g.add_node(nodeA)
if nodeB not in g.get_nodes(): g.add_node(nodeB)
if g.has_edge(nodeA,nodeB):
wt = g.get_edge_weight(nodeA,nodeB)
if bitscore > wt:
g.set_edge_weight(nodeA,nodeB,bitscore)
else:
pass
else:
# and create a new edge
g.add_edge(nodeA,nodeB,wt=bitscore)
# ready!
return g
