def group_novel_isoforms(new_isoforms, all_filter_passing_query_isoforms,
pred_samfile_path):
pred_samfile = pysam.AlignmentFile(pred_samfile_path, "r", check_sq=False)
query_new_isoforms = [
q_isoform for q_isoform in all_filter_passing_query_isoforms
if q_isoform.query_name in new_isoforms
]
G = nx.Graph()
for n in new_isoforms:
G.add_node(n)
print("nr new:", len(query_new_isoforms))
for i1 in query_new_isoforms:
for i2 in query_new_isoforms:
if i1.query_name == i2.query_name:
continue
else:
if is_same_isoform_cigar(i1, i2) and is_same_isoform_cigar(
i2, i1):
G.add_edge(i1.query_name, i2.query_name)
print(len(list(G.nodes())))
print(len(list(G.edges())))
maximal_cliques = [cl for cl in nx.find_cliques(G)]
print([len(cl) for cl in maximal_cliques])
print(sum([len(cl) for cl in maximal_cliques]))
print(len([len(cl) for cl in maximal_cliques]),
"unique splice sites isoforms")
queries_to_new = {
q_acc: "new_isoform_" + str(i)
for i, cl in enumerate(sorted(maximal_cliques, key=len))
for q_acc in cl
}
return queries_to_new
def get_cliques(netw, node):
g=nx.Graph(netw.subgraph(netw.neighbors(node).append(node)))
cliques = nx.find_cliques(g)
re=[]
for cli in cliques:
if node in cli and len(cli)>len(re):
re = cli
return re
def all_large_cliques_upto(G,limit=1000):
GG = G.copy()
cliq_iter = nx.find_cliques(GG)
for i in range(limit):
try:
cliq = []
while len(cliq)<3:
cliq = next(cliq_iter)
except StopIteration:
break
yield cliq
