def main(newick: str, output_newick: str, samples: Iterable[Sample]):
sample_name_by_workflow_run_id = {
str(s["workflow_run_id"]): s["sample_name"]
for s in samples
}
with open(newick) as i, open(output_newick, "w") as o:
tree = next(NewickIO.parse(i))
for node in tree.find_clades(order="level"):
node.name = sample_name_by_workflow_run_id.get(
node.name, node.name)
NewickIO.write([tree], o)
def read_fasta_or_newick_and_return_tree(path, nwk_path=None, patt=None):
global NUM_OF_VIRIONS
if any(path.name.endswith(x) for x in FASTA_EXTENSIONS):
seqs = AlignIO.read(path, FASTA)
seqs._records = [x for x in seqs if get_count(x, patt) > MIN_COUNT]
NUM_OF_VIRIONS = int(sum(get_count(x, patt) for x in seqs))
if len(seqs) <= 2: return None
tree = build_phylogenetic_tree(seqs)
if nwk_path is not None and tree is not None:
NewickIO.write([tree], nwk_path)
elif any(path.name.endswith(x) for x in NEWICK_EXTENSIONS):
tree = NewickIO.parse(path).next()
# Root the tree if necessary
if not tree.rooted:
tree.root_at_midpoint()
return tree
def main():
prog = sys.argv[0]
description = ('Parse newick tree an perform action on'
'each non-root node')
parser = argparse.ArgumentParser(prog=prog, description=description)
parser.add_argument('infile', nargs='?', type=argparse.FileType(),
help='a Newick treefile')
parser.add_argument('outfile', nargs='?', type=argparse.FileType('w'),
help='changed Newick outfile')
parser.add_argument('--cutoff', dest='cutoff', nargs='?', type=int, default=75,
help='value at or beneath which no inner node'
'confidences are snown any more')
options = parser.parse_args()
infile = options.infile or sys.stdin
outfile = options.outfile or sys.stdout
cutoff = options.cutoff
newick = NewickCutoff(infile, outfile, cutoff)
trees = newick.readtrees()
trees = newick.relabeltree(trees)
NewickIO.write(trees, outfile)
code)
if len(mappings) <= 0:
log.warning("empty mappings file")
return mappings
def printtrees(trees):
for tree in trees:
Phylo.draw_ascii(tree)
stdout_handler = logging.StreamHandler(sys.stderr)
handlers = [stdout_handler]
logging.basicConfig(level=logging.INFO,
format='[%(levelname)s - %(message)s]',
handlers=handlers)
log = logging.getLogger('LOGGER_NAME')
mappingfile = sys.argv[2]
mappings = readmappings(mappingfile)
mappedstrings = {}
treefile = sys.argv[1]
trees = readtrees(treefile)
trees = relabeltree(trees)
reportMappings(mappedstrings)
#printtees(trees)
NewickIO.write(trees, sys.stdout)
