def add_graph(graph1: GraphContainer, graph2: GraphContainer):
"""
Add all nodes, edges and paths from graph2 to graph1 (inplace)
"""
for node in graph2.refNodes():
graph1.add_refNode(
node["chrom"], node["start"], node["end"], node["sequences"])
for node in graph2.altNodes():
graph1.add_altNode(
node["chrom"], node["start"], node["end"], node["sequence"], node["sequences"])
for edge in graph2.edges.values():
graph1.add_edge(graph1.nodes[edge["from"]], graph1.nodes[edge["to"]], edge["sequences"])
graph1.paths += graph2.paths
def split_ref_nodes(graph: GraphContainer, max_len=300, padding_len=150):
"""
Split long reference nodes
:param graph: graph to work on
:param max_len: max length of reference node with no sequences
:param padding_len: length of sequence to keep
"""
assert max_len >= 2 * padding_len
for node in list(graph.refNodes()):
if node["end"] - node["start"] + 1 <= max_len:
continue
logging.info("Splitting long REF node: %s", node['name'])
firstEnd = node["start"] + padding_len - 1
n1 = graph.add_refNode(node["chrom"], node["start"], firstEnd, node["sequences"])
sndStart = node["end"] - padding_len + 1
n2 = graph.add_refNode(node["chrom"], sndStart, node["end"], node["sequences"])
for e in list(graph.inEdges(node)):
graph.add_edge(graph.nodes[e["from"]], n1, e["sequences"])
for e in list(graph.outEdges(node)):
graph.add_edge(n2, graph.nodes[e["to"]], e["sequences"])
graph.del_node(node)
