def load_tree_files(tree_dir):
"""Load trees from filepaths
checks if filenames indicate that trees are from different
distance methods. If so, warns user.
loads trees into phylonode objects
returns [trees]
raises a RuntimeError if no trees are loaded
"""
tree_file_names = os.listdir(tree_dir)
# ignore invisible files like .DS_Store
tree_file_names = [
fname for fname in tree_file_names if not fname.startswith('.')
]
# try to warn user if using multiple types of trees {
try:
base_names = []
for fname in tree_file_names:
base_names.append(parse_rarefaction_fname(fname)[0])
except ValueError:
pass
else:
if len(set(base_names)) > 1:
warnstr = """
warning: trees are named differently, please be sure you're not
comparing trees generated in different manners, unless you're quite sure
that's what you intend to do. types: """ + str(set(base_names)) + """
continuing anyway..."""
warn(warnstr)
# }
trees = []
for fname in tree_file_names:
try:
f = open(os.path.join(tree_dir, fname), 'U')
tree = TreeNode.from_newick(f)
tree.filepath = fname
trees.append(tree)
f.close()
except IOError as err:
sys.stderr.write('error loading tree ' + fname + '\n')
exit(1)
if len(trees) == 0:
raise RuntimeError('Error: no trees loaded' +
', check that tree directory has has valid trees')
return trees
def load_tree_files(tree_dir):
"""Load trees from filepaths
checks if filenames indicate that trees are from different
distance methods. If so, warns user.
loads trees into phylonode objects
returns [trees]
raises a RuntimeError if no trees are loaded
"""
tree_file_names = os.listdir(tree_dir)
# ignore invisible files like .DS_Store
tree_file_names = [fname for fname in tree_file_names if not
fname.startswith('.')]
# try to warn user if using multiple types of trees {
try:
base_names = []
for fname in tree_file_names:
base_names.append(parse_rarefaction_fname(fname)[0])
except ValueError:
pass
else:
if len(set(base_names)) > 1:
warnstr = """
warning: trees are named differently, please be sure you're not
comparing trees generated in different manners, unless you're quite sure
that's what you intend to do. types: """ + str(set(base_names)) + """
continuing anyway..."""
warn(warnstr)
# }
trees = []
for fname in tree_file_names:
try:
f = open(os.path.join(tree_dir, fname), 'U')
tree = TreeNode.from_newick(f)
tree.filepath = fname
trees.append(tree)
f.close()
except IOError as err:
sys.stderr.write('error loading tree ' + fname + '\n')
exit(1)
if len(trees) == 0:
raise RuntimeError('Error: no trees loaded' +
', check that tree directory has has valid trees')
return trees
def make_output_row(f_metrics, metric, f_samples, f_data, fname, num_cols, all_samples):
f_col = f_metrics.index(metric)
# first 3 cols are fname, seqs/sample, iteration
try:
base, seqs, iter, ext = parse_rarefaction_fname(fname)
except:
seqs, iter = "n/a", "n/a"
output_row = [fname] + ["n/a"] * num_cols
for f_row, sample in enumerate(f_samples):
try:
output_row[all_samples.index(sample) + 1] = str(f_data[f_row, f_col])
except IndexError:
print("warning, didn't find sample in example file." + "exiting", sample, fname, metric)
raise # re-raise error
output_row.insert(1, seqs)
output_row.insert(2, iter)
return output_row
def make_output_row(f_metrics, metric, f_samples, f_data, fname, num_cols, all_samples):
f_col = f_metrics.index(metric)
# first 3 cols are fname, seqs/sample, iteration
try:
base, seqs, iter, ext = parse_rarefaction_fname(fname)
except:
seqs, iter = 'n/a', 'n/a'
output_row = [fname] + ['n/a']*num_cols
for f_row, sample in enumerate(f_samples):
try:
output_row[all_samples.index(sample)+1] = \
str(f_data[f_row,f_col])
except IndexError:
print("warning, didn't find sample in example file."+\
"exiting", sample, fname, metric)
raise # re-raise error
output_row.insert(1, seqs)
output_row.insert(2, iter)
return output_row
def test_parse_rarefaction_fname(self):
""" parse_rarefaction_fname should return base, seqs/sam, iters, etc."""
fname = "alpha_rarefaction_900_3.txt"
base, seqs, iter, ext = parse_rarefaction_fname(fname)
self.assertEqual((base, seqs, iter, ext),
("alpha_rarefaction", 900, 3, ".txt"))
def test_parse_rarefaction_fname(self):
""" parse_rarefaction_fname should return base, seqs/sam, iters, etc."""
fname = "alpha_rarefaction_900_3.txt"
base, seqs, iter, ext = parse_rarefaction_fname(fname)
self.assertEqual((base, seqs, iter, ext),
("alpha_rarefaction", 900, 3, ".txt"))
