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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.
from __future__ import print_function
from Bio import MissingExternalDependencyError
import sys
import os
import itertools
from Bio._py3k import StringIO
from Bio._py3k import zip
from Bio import SeqIO
from Bio import Phylo
from Bio.Phylo.Applications import FastTreeCommandline
from Bio.Phylo.Applications import _Fasttree
from Bio.Application import ApplicationError
#################################################################
# 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 Bio._py3k 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("%s -help" % filename)
# 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.")
#################################################################
print("Checking error conditions")
print("=========================")
print("Empty file")
input_file = "does_not_exist.fasta"
assert not os.path.isfile(input_file)
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
stdout, stderr = cline()
assert False, "Should have failed, returned:\n%s\n%s" % (stdout, stderr)
except ApplicationError as err:
print("Failed (good)")
# Python 2.3 on Windows gave (0, 'Error')
# Python 2.5 on Windows gives [Errno 0] Error
assert "Cannot open sequence file" in str(err) or \
"Cannot open input file" in str(err) or \
"Non-zero return code " in str(err), str(err)
print("")
print("Single sequence")
input_file = "Fasta/f001"
assert os.path.isfile(input_file)
assert len(list(SeqIO.parse(input_file, "fasta"))) == 1
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
stdout, stderr = cline()
if "Unique: 1/1" in stderr:
print("Failed (good)")
else:
assert False, "Should have failed, returned:\n%s\n%s" % (stdout, stderr)
except ApplicationError as err:
print("Failed (good)")
# assert str(err) == "No records found in handle", str(err)
print("")
print("Invalid sequence")
input_file = "Medline/pubmed_result1.txt"
assert os.path.isfile(input_file)
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
stdout, stderr = cline()
assert False, "Should have failed, returned:\n%s\n%s" % (stdout, stderr)
except ApplicationError as err:
print("Failed (good)")
# Ideally we'd catch the return code and raise the specific
# error for "invalid format", rather than just notice there
# is not output file.
# Note:
# Python 2.3 on Windows gave (0, 'Error')
# Python 2.5 on Windows gives [Errno 0] Error
assert "invalid format" in str(err) \
or "not produced" in str(err) \
or "No sequences in file" in str(err) \
or "Non-zero return code " in str(err), str(err)
#################################################################
print("")
print("Checking normal situations")
print("==========================")
# Create a temp fasta file with a space in the name
temp_filename_with_spaces = "Clustalw/temp horses.fasta"
handle = open(temp_filename_with_spaces, "w")
SeqIO.write(SeqIO.parse("Phylip/hennigian.phy", "phylip"), handle, "fasta")
handle.close()
for input_file in ["Quality/example.fasta", "Clustalw/temp horses.fasta"]:
input_records = SeqIO.to_dict(SeqIO.parse(input_file, "fasta"))
print("")
print("Calling fasttree on %s (with %i records)"
% (repr(input_file), len(input_records)))
# Any filesnames with spaces should get escaped with quotes automatically.
# Using keyword arguments here.
cline = _Fasttree.FastTreeCommandline(fasttree_exe, input=input_file, nt=True)
assert str(eval(repr(cline))) == str(cline)
out, err = cline()
assert err.strip().startswith("FastTree")
print("")
print("Checking generation of tree terminals")
tree = Phylo.read(StringIO(out), 'newick')
def lookup_by_names(tree):
names = {}
for clade in tree.find_clades():
if clade.name:
if clade.name in names:
raise ValueError("Duplicate key: %s" % clade.name)
names[clade.name] = clade
return names
names = lookup_by_names(tree)
assert len(names) > 0.0
print("Success")
print("")
print("Checking distances between tree terminals")
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):
assert dist > 0.0
print("Success")
print("")
print("Done")
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