diff options
Diffstat (limited to 'pangraph/graph.py')
| -rw-r--r-- | pangraph/graph.py | 16 |
1 files changed, 13 insertions, 3 deletions
diff --git a/pangraph/graph.py b/pangraph/graph.py index c4e3f83..d154f74 100644 --- a/pangraph/graph.py +++ b/pangraph/graph.py @@ -518,12 +518,22 @@ class Graph(object): tmp[1].flush() def make_tree(n): - proc = subprocess.Popen(f"mafft --auto {path[n]} | fasttree", + proc = [None, None] + out = [None, None] + err = [None, None] + proc[0] = subprocess.Popen(f"mafft --auto {path[n]}", stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) - out, err = proc.communicate() - tree = Phylo.read(io.StringIO(out.decode('utf-8')), format='newick') + proc[1] = subprocess.Popen(f"fasttree", + stdin =subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + shell=True) + out[0], err[0] = proc[0].communicate() + out[1], err[1] = proc[1].communicate(input=out[0]) + tree = Phylo.read(io.StringIO(out[1].decode('utf-8')), format='newick') + print(f"ALIGNMENT=\n{out[0]}") print(f"SCORE={tree.total_branch_length()/(2*num_seqs)}", end=";") make_tree(0) |