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# Copyright 2013 by Nate Sutton. All rights reserved.
# Based on test_Clustalw_tool.py by Peter Cock.
# Example code used from Biopython's Phylo cookbook by Eric Talevich.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for Fasttree tool."""
import itertools
import os
import sys
import unittest
import warnings
from io import StringIO
from Bio import BiopythonDeprecationWarning
from Bio import MissingExternalDependencyError
from Bio import Phylo
from Bio import SeqIO
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
from Bio.Application import ApplicationError
from Bio.Phylo.Applications import _Fasttree
from Bio.Phylo.Applications import FastTreeCommandline
#################################################################
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"
fasttree_exe = None
if sys.platform == "win32":
try:
# This can vary depending on the Windows language.
prog_files = os.environ["PROGRAMFILES"]
except KeyError:
prog_files = r"C:\Program Files (x86)"
# A default fasttree file path of "C:\Program Files (x86)\Fasttree.exe"
# was chosen here but users can alter the path according to where
# fasttree is located on their systems
likely_dirs = ["", "FastTree"]
likely_exes = ["FastTree.exe"]
for folder in likely_dirs:
if os.path.isdir(os.path.join(prog_files, folder)):
for filename in likely_exes:
if os.path.isfile(os.path.join(prog_files, folder, filename)):
fasttree_exe = os.path.join(prog_files, folder, filename)
break
if fasttree_exe:
break
else:
from subprocess import getoutput
# Website uses 'FastTree', Nate's system had 'fasttree'
likely_exes = ["FastTree", "fasttree"]
for filename in likely_exes:
# Checking the -help argument
output = getoutput(f"{filename} -help")
# Since "is not recognized" may be in another language, try and be sure this
# is really the fasttree tool's output
if (
"is not recognized" not in output
and "protein_alignment" in output
and "nucleotide_alignment" in output
):
fasttree_exe = filename
break
if not fasttree_exe:
raise MissingExternalDependencyError(
"Install FastTree and correctly set the file path to the program "
"if you want to use it from Biopython."
)
class FastTreeTestCase(unittest.TestCase):
def check(self, path, length):
input_records = SeqIO.to_dict(SeqIO.parse(path, "fasta"))
self.assertEqual(len(input_records), length)
# Any filenames with spaces should get escaped with quotes
# automatically.
# Using keyword arguments here.
cline = _Fasttree.FastTreeCommandline(fasttree_exe, input=path, nt=True)
self.assertEqual(str(eval(repr(cline))), str(cline))
out, err = cline()
self.assertTrue(err.strip().startswith("FastTree"))
tree = Phylo.read(StringIO(out), "newick")
names = {}
for clade in tree.find_clades():
if clade.name:
self.assertNotIn(clade.name, names)
names[clade.name] = clade
self.assertGreater(len(names), 0)
def terminal_neighbor_dists(self):
"""Return a list of distances between adjacent terminals."""
def generate_pairs(self):
pairs = itertools.tee(self)
next(pairs[1]) # Advance second iterator one step
return zip(pairs[0], pairs[1])
return [
self.distance(*i)
for i in generate_pairs(self.find_clades(terminal=True))
]
for dist in terminal_neighbor_dists(tree):
self.assertGreater(dist, 0.0)
def test_normal(self):
self.check("Quality/example.fasta", 3)
def test_filename_spaces(self):
path = "Clustalw/temp horses.fasta" # note spaces in filename
records = SeqIO.parse("Phylip/hennigian.phy", "phylip")
with open(path, "w") as handle:
length = SeqIO.write(records, handle, "fasta")
self.assertEqual(length, 10)
self.check(path, length)
def test_invalid(self):
path = "Medline/pubmed_result1.txt"
cline = FastTreeCommandline(fasttree_exe, input=path)
with self.assertRaises(ApplicationError) as cm:
stdout, stderr = cline()
message = str(cm.exception)
self.assertTrue(
"invalid format" in message
or "not produced" in message
or "No sequences in file" in message
or "Error parsing header line:" in message
or "Non-zero return code " in message,
msg=f"Unknown ApplicationError raised: {message}",
)
def test_single(self):
path = "Fasta/f001"
records = list(SeqIO.parse(path, "fasta"))
self.assertEqual(len(records), 1)
cline = FastTreeCommandline(fasttree_exe, input=path)
stdout, stderr = cline()
self.assertIn("Unique: 1/1", stderr)
def test_empty(self):
path = "does_not_exist.fasta"
cline = FastTreeCommandline(fasttree_exe, input=path)
with self.assertRaises(ApplicationError) as cm:
stdout, stderr = cline()
message = str(cm.exception)
self.assertTrue(
"Cannot open sequence file" in message
or "Cannot open sequence file" in message
or f"Cannot read {path}" in message
or "Non-zero return code " in message,
msg=f"Unknown ApplicationError raised: {message}",
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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