diff options
Diffstat (limited to 'pangraph/tree.py')
| -rw-r--r-- | pangraph/tree.py | 13 |
1 files changed, 10 insertions, 3 deletions
diff --git a/pangraph/tree.py b/pangraph/tree.py index 605bac3..d36b77d 100644 --- a/pangraph/tree.py +++ b/pangraph/tree.py @@ -139,6 +139,11 @@ class Clade(object): 'fapath' : self.fapath, 'graph' : serialize(self.graph) if self.graph is not None else None } + def set_level(self, level): + for c in self.child: + c.set_level(level+1) + self.level = level + class Tree(object): # ------------------- # Class constructor @@ -287,7 +292,8 @@ class Tree(object): leafs = {n.name: n for n in self.get_leafs()} self.seqs = {leafs[name]:seq for name,seq in seqs.items()} - def align(self, tmpdir, min_blk_len, mu, beta, extensive, log_stats=False, verbose=False): + def align(self, tmpdir, min_blk_len, mu, beta, extensive, edge_window, edge_extend, log_stats=False, verbose=False): + self.root.set_level(0) # NOTE: for debug logging stats = {} # --------------------------------------------- # internal functions @@ -345,7 +351,7 @@ class Tree(object): graph1, fapath1 = node1.graph, node1.fapath graph2, fapath2 = node2.graph, node2.fapath graph = Graph.fuse(graph1, graph2) - graph, _ = graph.union(fapath1, fapath2, f"{tmpdir}/{n.name}", min_blk_len, mu, beta, extensive) + graph, _ = graph.union(fapath1, fapath2, f"{tmpdir}/{n.name}", min_blk_len, mu, beta, extensive, edge_window, edge_extend) else: graph = node1.graph @@ -355,7 +361,7 @@ class Tree(object): itr = f"{tmpdir}/{n.name}_iter_{i}" with open(f"{itr}.fa", 'w') as fd: graph.write_fasta(fd) - graph, contin = graph.union(itr, itr, f"{tmpdir}/{n.name}_iter_{i}", min_blk_len, mu, beta, extensive) + graph, contin = graph.union(itr, itr, f"{tmpdir}/{n.name}_iter_{i}", min_blk_len, mu, beta, extensive, edge_window, edge_extend) if not contin: return graph return graph @@ -377,6 +383,7 @@ class Tree(object): for n in self.postorder(): if n.is_leaf(): continue + print(f"+++LEVEL={n.level}+++") n.fapath = f"{tmpdir}/{n.name}" log(f"fusing {n.child[0].name} with {n.child[1].name} @ {n.name}") n.graph = merge(*n.child) |