# use home-made code to prune the tree instead
treeName, treeExt = splitext(outtrees)
fName, ext = splitext(outtrees)
for i, RS in enumerate(removing_sets):
trees_shrinked = deepcopy(trees)
outfile = outdir + "/" + fName + "_RS_" + quantiles[i]
with open(outfile, 'w') as f:
for item in RS:
for s in item:
f.write(s + "\t")
f.write("\n")
for t, tree in enumerate(trees_shrinked):
#filt = lambda node: False if (node.taxon is not None and node.taxon.label in RS[t]) else True
#tree.filter_leaf_nodes(filt,update_bipartitions=True)
prune_tree(tree, RS[t])
trees_shrinked.write_to_path(
outdir + "/" + treeName + "_" + quantiles[i] + treeExt, 'newick')
if not args["tempdir"]:
call(["rm", "-r", tempdir])
'''
# prune trees according to the removing sets.
# calling nw_prune here as a (terrible) temporary sollution, because Dendropy's filter_leaf_nodes() seems to have problems
fName,ext = splitext(outtrees)
for i,RS in enumerate(removing_sets):
outfile = outdir + "/" + fName + "_RS_" + quantiles[i]
with open(outfile,'w') as f:
for item in RS:
for s in item:
parser.add_argument("-l", "--listing", required=True, help="Removing set")
parser.add_argument(
"-v",
"--reverse",
required=False,
action='store_true',
help="Do the reverse pruning: retain the listed taxa. Default: NO")
args = vars(parser.parse_args())
RS = args["listing"].split() if not args["reverse"] else None
with open(args["input"], 'r') as fin:
treein = fin.readlines()
treeout = []
for t in treein:
tree = Tree.get(data=t, schema="newick", preserve_underscores=True)
if not RS:
RS = [
x.taxon.label for x in tree.leaf_node_iter()
if x.taxon.label not in args["listing"].split()
]
prune_tree(tree, RS)
treeout.append(tree.as_string("newick", unquoted_underscores=True))
with open(args["output"], 'w') as fout:
for t in treeout:
fout.write(t)
print("The tree is not large enough for this sampling size!")
else:
if outfile:
fout_info = open(outfile, 'w')
else:
fout_info = stdout
fout_info.write("Sampled from " + abspath(treefile) + "\n")
fout_info.write("Sampled " + str(n_reps) + " replicate(s) of " +
str(n_ingroups) + " ingroup(s) and " + str(n_outgroups) +
" outgroup(s)\n")
with open(outtreeFile, 'w') as fout_tree:
for i, (t, igs, ogs) in enumerate(samples):
fout_info.write("Rep " + str(i + 1) + ":\n")
fout_info.write("Ingroups: ")
for i in igs:
fout_info.write(i + " ")
fout_info.write("\nOutgroups: ")
for o in ogs:
fout_info.write(o + " ")
fout_info.write("\n")
fout_tree.write(t.as_string('newick'))
fout_info.close()
if outtree_noOG:
with open(outtree_noOG, 'w') as f:
for t, igs, ogs in samples:
prune_tree(t, ogs)
f.write(t.as_string('newick'))