def __init__(self):
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
phyml_exe = None
exename = "PhyML-3.1_win32.exe" if sys.platform == "win32" else "phyml"
from Bio._py3k import getoutput
try:
output = getoutput(exename + " --version")
if "not found" not in output and "20" in output:
phyml_exe = exename
except OSError:
# Python 2.6 or 2.7 on Windows XP:
# WindowsError: [Error 2] The system cannot find the file specified
# Python 3.3 or 3.4 on Windows XP:
# FileNotFoundError: [WinError 2] The system cannot find the file
# specified
pass
if not phyml_exe:
raise MissingExternalDependencyError(
"Install PhyML 3.0 if you want to use the \
Bio.Phylo.Applications wrapper.")
# Example Phylip file with 13 aligned protein sequences
EX_PHYLIP = 'HTR1E_aligned.phy'
self.EX_PHYLIP = EX_PHYLIP
def raxml(sequences,
starting_tree="pars",
model="JC",
bootstrap=False,
fixed_tree=False,
bstrees=100,
log=True):
raxml_exe = None
try:
from Bio._py3k import getoutput
output = getoutput("raxml-ng -v")
if "not found" not in output and "RAxML-NG" in output:
raxml_exe = "raxml-ng"
except OSError:
pass
if not raxml_exe:
raise MissingExternalDependencyError(
"Install RAxML (binary raxml-ng) if you want to test the Bio.Phylo.Applications wrapper."
)
if not fixed_tree:
if bootstrap:
cmd = RaxmlCommandline(raxml_exe,
bootstrap=None,
sequences=sequences,
model=model,
starting_tree=starting_tree,
bstrees=bstrees)
else:
cmd = RaxmlCommandline(raxml_exe,
sequences=sequences,
model=model,
starting_tree=starting_tree)
else:
cmd = RaxmlCommandline(raxml_exe,
fixtree=None,
sequences=sequences,
model=model,
starting_tree=starting_tree)
out, err = cmd()
if log:
print out
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for Bio.Phylo.Applications wrappers."""
import os
import unittest
from Bio import Phylo
from Bio.Phylo.Applications import RaxmlCommandline
from Bio import MissingExternalDependencyError
raxml_exe = None
try:
from Bio._py3k import getoutput
output = getoutput("raxmlHPC -v")
if "not found" not in output and "This is RAxML" in output:
raxml_exe = "raxmlHPC"
except OSError:
# TODO: Use FileNotFoundError once we drop Python 2
pass
if not raxml_exe:
raise MissingExternalDependencyError(
"Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.")
# Example Phylip file with 4 aligned protein sequences
EX_PHYLIP = "Phylip/interlaced2.phy"
class AppTests(unittest.TestCase):
import os
import unittest
from Bio import SeqIO
from Bio import AlignIO
from Bio.Align.Applications import ClustalOmegaCommandline
from Bio.Application import ApplicationError
#################################################################
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
clustalo_exe = None
from Bio._py3k import getoutput
try:
output = getoutput("clustalo --help")
if output.startswith("Clustal Omega"):
clustalo_exe = "clustalo"
except OSError:
# TODO: Use FileNotFoundError once we drop Python 2
pass
if not clustalo_exe:
raise MissingExternalDependencyError(
"Install clustalo if you want to use Clustal Omega from Biopython.")
class ClustalOmegaTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
import sys
import os
import unittest
from Bio import MissingExternalDependencyError
from Bio.Align.Applications import DialignCommandline
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"
dialign_exe = None
if sys.platform == "win32":
raise MissingExternalDependencyError("DIALIGN2-2 not available on Windows")
else:
from Bio._py3k import getoutput
output = getoutput("dialign2-2")
if "not found" not in output and "dialign2-2" in output.lower():
dialign_exe = "dialign2-2"
if "DIALIGN2_DIR" not in os.environ:
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR for DIALIGN2-2 missing.")
if not os.path.isdir(os.environ["DIALIGN2_DIR"]):
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR for DIALIGN2-2 is not a valid directory.")
if not os.path.isfile(os.path.join(os.environ["DIALIGN2_DIR"], "BLOSUM")):
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR directory missing BLOSUM file.")
# TODO - check for tp400_dna, tp400_prot and tp400_trans too?
if not dialign_exe:
raise MissingExternalDependencyError(
prog_files,
os.path.join(prog_files,"Muscle3.6"),
os.path.join(prog_files,"Muscle3.7"),
os.path.join(prog_files,"Muscle3.8"),
os.path.join(prog_files,"Muscle3.9"),
os.path.join(prog_files,"Muscle")] + sys.path
for folder in likely_dirs:
if os.path.isdir(folder):
if os.path.isfile(os.path.join(folder, "muscle.exe")):
muscle_exe = os.path.join(folder, "muscle.exe")
break
if muscle_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("muscle -version")
#Since "not found" may be in another language, try and be sure this is
#really the MUSCLE tool's output
if "not found" not in output and "MUSCLE" in output \
and "Edgar" in output:
muscle_exe = "muscle"
if not muscle_exe:
raise MissingExternalDependencyError(
"Install MUSCLE if you want to use the Bio.Align.Applications wrapper.")
#################################################################
class MuscleApplication(unittest.TestCase):
prog_files = os.environ["PROGRAMFILES"]
except KeyError:
prog_files = r"C:\Program Files"
likely_dirs = ["bwa", "bwa-0.6.2", ""]
likely_exes = ["bwa"]
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)):
bwa_exe = os.path.join(prog_files, folder, filename)
break
if bwa_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("bwa")
# Since "not found" may be in another language, try and be sure this is
# really the bwa tool's output
bwa_found = False
if "not found" not in output and "bwa" in output \
and "alignment via Burrows-Wheeler transformation" in output:
bwa_exe = "bwa"
skip_aln_tests = False
aln_output = getoutput("bwa aln")
if "unrecognized" in aln_output:
skip_aln_tests = True
print("'bwa aln' is unrecognized, skipping aln/samse/sampe tests")
if not bwa_exe:
raise MissingExternalDependencyError("Install bwa and correctly set"
import sys
import os
import unittest
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import TCoffeeCommandline
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
t_coffee_exe = None
if sys.platform == "win32":
raise MissingExternalDependencyError(
"Testing TCOFFEE on Windows not supported yet")
else:
from Bio._py3k import getoutput
output = getoutput("t_coffee -version")
if "not found" not in output \
and ("t_coffee" in output.lower() or "t-coffee" in output.lower()):
t_coffee_exe = "t_coffee"
if not t_coffee_exe:
raise MissingExternalDependencyError(
"Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.")
class TCoffeeApplication(unittest.TestCase):
def setUp(self):
self.infile1 = "Fasta/fa01"
self.outfile1 = "fa01.aln"
self.outfile2 = "fa01.html" # Written by default when no output set
# fasttree is located on their systems
likely_dirs = ["Fasttree", "fasttree", "FastTree"]
likely_exes = ["Fasttree.exe", "fasttree.exe", "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
# Checking the -help argument
output = getoutput("fasttree -help")
# Since "is not recognized" may be in another language, try and be sure this
# is really the fasttree tool's output
fasttree_found = False
if "is not recognized" not in output and "protein_alignment" in output \
and "nucleotide_alignment" in output:
fasttree_exe = "fasttree"
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")
#!/usr/bin/env python
# Copyright 2004 by Michael Hoffman. All rights reserved. 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 Bio import MissingExternalDependencyError
import sys
if sys.platform=="win32":
# Someone needs to find out if dnal works nicely on windows,
# and if so where it is typically installed.
raise MissingExternalDependencyError(
"Don't know how to find the Wise2 tool dnal on Windows.")
from Bio._py3k import getoutput
not_found_types = ["command not found", "dnal: not found", "not recognized"]
dnal_output = getoutput("dnal")
for not_found in not_found_types:
if not_found in dnal_output:
#raise MissingExternalDependencyError(dnal_output)
raise MissingExternalDependencyError(
"Install Wise2 (dnal) if you want to use Bio.Wise.")
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Unit tests for the Bio.PDB.ResidueDepth module."""
import unittest
import warnings
from Bio.PDB import PDBParser, ResidueDepth
from Bio import MissingExternalDependencyError
from Bio.PDB.PDBExceptions import PDBConstructionWarning
from Bio._py3k import getoutput
msms_exe = None
try:
output = getoutput("msms -h")
if output.startswith("Usage : msms parameters"):
msms_exe = "msms"
except OSError:
pass
if not msms_exe:
raise MissingExternalDependencyError(
"Install MSMS if you want to use it in Biopython.")
class ResidueDepthTests(unittest.TestCase):
"""Test ResidueDepth module."""
def check_msms(self, prot_file, first_100_residues):
p = PDBParser()
#!/usr/bin/env python
# Copyright 2004 by Michael Hoffman. All rights reserved. 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 Bio import MissingExternalDependencyError
import sys
if sys.platform == "win32":
# Someone needs to find out if dnal works nicely on windows,
# and if so where it is typically installed.
raise MissingExternalDependencyError(
"Don't know how to find the Wise2 tool dnal on Windows.")
from Bio._py3k import getoutput
not_found_types = ["command not found", "dnal: not found", "not recognized"]
dnal_output = getoutput("dnal")
for not_found in not_found_types:
if not_found in dnal_output:
raise MissingExternalDependencyError(
"Install Wise2 (dnal) if you want to use Bio.Wise.")
import sys
import os
import unittest
from Bio._py3k import StringIO
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import ProbconsCommandline
#Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
probcons_exe = None
if sys.platform=="win32":
raise MissingExternalDependencyError("PROBCONS not available on Windows")
else:
from Bio._py3k import getoutput
output = getoutput("probcons")
if "not found" not in output and "probcons" in output.lower():
probcons_exe = "probcons"
if not probcons_exe:
raise MissingExternalDependencyError(
"Install PROBCONS if you want to use the Bio.Align.Applications wrapper.")
class ProbconsApplication(unittest.TestCase):
def setUp(self):
self.infile1 = "Fasta/fa01"
self.annotation_outfile = "Fasta/probcons_annot.out"
def tearDown(self):
# fasttree is located on their systems
likely_dirs = ["Fasttree", "fasttree", "FastTree"]
likely_exes = ["Fasttree.exe", "fasttree.exe", "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
# Checking the -help argument
output = getoutput("fasttree -help")
# Since "is not recognized" may be in another language, try and be sure this
# is really the fasttree tool's output
fasttree_found = False
if "is not recognized" not in output and "protein_alignment" in output \
and "nucleotide_alignment" in output:
fasttree_exe = "fasttree"
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")
prog_files = r"C:\Program Files"
# By default tries C:\Program Files\samtools\samtools.exe
# or C:\Program Files\samtools.exe was chosen
likely_dirs = ["samtools", ""]
likely_exes = ["samtools.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)):
samtools_exe = os.path.join(prog_files, folder, filename)
break
if samtools_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("samtools")
# Since "not found" may be in another language, try and be sure this is
# really the samtools tool's output
if ("not found" not in output
and "samtools (Tools for alignments in the SAM format)" in output):
samtools_exe = "samtools"
if not samtools_exe:
raise MissingExternalDependencyError(
"""Install samtools and correctly set the file path to the program
if you want to use it from Biopython""")
class SamtoolsTestCase(unittest.TestCase):
"""Class for implementing Samtools test cases."""
import sys
import os
import unittest
from Bio import MissingExternalDependencyError
from Bio.Align.Applications import DialignCommandline
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
dialign_exe = None
if sys.platform == "win32":
raise MissingExternalDependencyError("DIALIGN2-2 not available on Windows")
else:
from Bio._py3k import getoutput
output = getoutput("dialign2-2")
if "not found" not in output and "dialign2-2" in output.lower():
dialign_exe = "dialign2-2"
if "DIALIGN2_DIR" not in os.environ:
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR for DIALIGN2-2 missing.")
if not os.path.isdir(os.environ["DIALIGN2_DIR"]):
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR for DIALIGN2-2 is not a valid directory.")
if not os.path.isfile(os.path.join(os.environ["DIALIGN2_DIR"], "BLOSUM")):
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR directory missing BLOSUM file.")
# TODO - check for tp400_dna, tp400_prot and tp400_trans too?
if not dialign_exe:
raise MissingExternalDependencyError(
#A default path of C:\Program Files\bwa.exe was chosen
#but this path can be edited depending on where bwa is located
likely_dirs = ["bwa", "BWA", "Bwa", "bwa-0.6.2"]
likely_exes = ["bwa.exe", "BWA.exe", "Bwa.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)):
bwa_exe = os.path.join(prog_files, folder, filename)
break
if bwa_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("bwa")
#Since "not found" may be in another language, try and be sure this is
#really the bwa tool's output
bwa_found = False
if "not found" not in output and "bwa" in output \
and "alignment via Burrows-Wheeler transformation" in output:
bwa_exe = "bwa"
if not bwa_exe:
raise MissingExternalDependencyError(\
"Install bwa and correctly set the file path to the program if you want to use it from Biopython")
class BwaTestCase(unittest.TestCase):
"""Class for implementing BWA test cases"""
# EMBOSS also sets an environment variable which we will check for.
path = os.environ["EMBOSS_ROOT"]
if os.path.isdir(path):
for name in exes_wanted:
if os.path.isfile(os.path.join(path, name + ".exe")):
exes[name] = os.path.join(path, name + ".exe")
del name
else:
raise MissingExternalDependencyError(
"$EMBOSS_ROOT=%r which does not exist!" % path)
del path
if sys.platform != "win32":
from Bio._py3k import getoutput
for name in exes_wanted:
# This will "just work" if installed on the path as normal on Unix
output = getoutput("%s -help" % name)
if "not found" not in output and "not recognized" not in output:
exes[name] = name
del output
del name
if len(exes) < len(exes_wanted):
raise MissingExternalDependencyError(
"Install EMBOSS if you want to use Bio.Emboss.")
def get_emboss_version():
"""Returns a tuple of three ints, e.g. (6,1,0)"""
# Windows and Unix versions of EMBOSS seem to differ in
# which lines go to stdout and stderr - so merge them.
child = subprocess.Popen(_escape_filename(exes["embossversion"]),
import unittest
from Bio import Phylo
from Bio.Phylo.Applications import PhymlCommandline
from Bio import MissingExternalDependencyError
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
phyml_exe = None
if sys.platform=="win32":
raise MissingExternalDependencyError(
"Testing PhyML on Windows not supported yet")
else:
from Bio._py3k import getoutput
output = getoutput("phyml --version")
if "not found" not in output and "20" in output:
phyml_exe = "phyml"
if not phyml_exe:
raise MissingExternalDependencyError(
"Install PhyML 3.0 if you want to use the Bio.Phylo.Applications wrapper.")
# Example Phylip file with 4 aligned protein sequences
EX_PHYLIP = 'Phylip/interlaced2.phy'
class AppTests(unittest.TestCase):
"""Tests for application wrappers."""
import sys
import os
import unittest
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import TCoffeeCommandline
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"
t_coffee_exe = None
if sys.platform == "win32":
raise MissingExternalDependencyError(
"Testing TCOFFEE on Windows not supported yet")
else:
from Bio._py3k import getoutput
output = getoutput("t_coffee -version")
if "not found" not in output \
and ("t_coffee" in output.lower()
or "t-coffee" in output.lower()):
t_coffee_exe = "t_coffee"
if not t_coffee_exe:
raise MissingExternalDependencyError(
"Install TCOFFEE if you want to use the Bio.Align.Applications wrapper."
)
class TCoffeeApplication(unittest.TestCase):
def setUp(self):
self.infile1 = "Fasta/fa01"
# TODO: Use a temp dir for the output files:
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Unit tests for the Bio.PDB.ResidueDepth module."""
import unittest
import warnings
from Bio.PDB import PDBParser, ResidueDepth
from Bio import MissingExternalDependencyError
from Bio.PDB.PDBExceptions import PDBConstructionWarning
from Bio._py3k import getoutput
msms_exe = None
try:
output = getoutput("msms -h")
if output.startswith("Usage : msms parameters"):
msms_exe = "msms"
except OSError:
pass
if not msms_exe:
raise MissingExternalDependencyError(
"Install MSMS if you want to use it in Biopython.")
class ResidueDepthTests(unittest.TestCase):
"""Test ResidueDepth module."""
def check_msms(self, prot_file, first_100_residues):
p = PDBParser()
with warnings.catch_warnings():
import unittest
from Bio import AlignIO
from Bio import MissingExternalDependencyError
from Bio import SeqIO
from Bio.Align.Applications import MSAProbsCommandline
from Bio.Application import ApplicationError
from Bio._py3k import getoutput
#################################################################
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
msaprobs_exe = None
try:
output = getoutput("msaprobs -version")
if output.startswith("MSAPROBS version"):
msaprobs_exe = "msaprobs"
except OSError:
# TODO: Use FileNotFoundError once we drop Python 2
pass
if not msaprobs_exe:
raise MissingExternalDependencyError(
"Install msaprobs if you want to use MSAProbs from Biopython.")
class MSAProbsTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
import unittest
from Bio import AlignIO
from Bio import MissingExternalDependencyError
from Bio import SeqIO
from Bio.Align.Applications import MSAProbsCommandline
from Bio.Application import ApplicationError
from Bio._py3k import getoutput
#################################################################
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"
msaprobs_exe = None
try:
output = getoutput("msaprobs -version")
if output.startswith("MSAPROBS version"):
msaprobs_exe = "msaprobs"
except OSError:
# TODO: Use FileNotFoundError once we drop Python 2
pass
if not msaprobs_exe:
raise MissingExternalDependencyError(
"Install msaprobs if you want to use MSAProbs from Biopython.")
class MSAProbsTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
from Bio import MissingExternalDependencyError
from Bio import SeqIO
from Bio.Application import ApplicationError
from Bio.Motif.Applications import XXmotifCommandline
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
xxmotif_exe = None
if sys.platform == "win32":
# TODO
raise MissingExternalDependencyError(
"Testing this on Windows is not implemented yet")
else:
from Bio._py3k import getoutput
output = getoutput("XXmotif")
if output.find("== XXmotif version") != -1:
xxmotif_exe = "XXmotif"
if not xxmotif_exe:
raise MissingExternalDependencyError(
"Install XXmotif if you want to use XXmotif from Biopython.")
class XXmotifTestCase(unittest.TestCase):
def setUp(self):
self.out_dir = "xxmotif-temp"
self.files_to_clean = set()
def tearDown(self):
for filename in self.files_to_clean:
import unittest
from Bio import Phylo
from Bio.Phylo.Applications import PhymlCommandline
from Bio import MissingExternalDependencyError
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
phyml_exe = None
if sys.platform == "win32":
raise MissingExternalDependencyError(
"Testing PhyML on Windows not supported yet")
else:
from Bio._py3k import getoutput
output = getoutput("phyml --version")
if "not found" not in output and "20" in output:
phyml_exe = "phyml"
if not phyml_exe:
raise MissingExternalDependencyError(
"Install PhyML 3.0 if you want to use the Bio.Phylo.Applications wrapper."
)
# Example Phylip file with 4 aligned protein sequences
EX_PHYLIP = 'Phylip/interlaced2.phy'
class AppTests(unittest.TestCase):
"""Tests for application wrappers."""
def test_phyml(self):
prog_files = os.environ["PROGRAMFILES"]
except KeyError:
prog_files = r"C:\Program Files"
likely_dirs = ["bwa", "bwa-0.6.2", ""]
likely_exes = ["bwa"]
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)):
bwa_exe = os.path.join(prog_files, folder, filename)
break
if bwa_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("bwa")
# Since "not found" may be in another language, try and be sure this is
# really the bwa tool's output
bwa_found = False
if "not found" not in output and "bwa" in output \
and "alignment via Burrows-Wheeler transformation" in output:
bwa_exe = "bwa"
skip_aln_tests = False
aln_output = getoutput("bwa aln")
if "unrecognized" in aln_output:
skip_aln_tests = True
print("'bwa aln' is unrecognized, skipping aln/samse/sampe tests")
if not bwa_exe:
raise MissingExternalDependencyError("Install bwa and correctly set"
os.path.join(prog_files, "Muscle3.6"),
os.path.join(prog_files, "Muscle3.7"),
os.path.join(prog_files, "Muscle3.8"),
os.path.join(prog_files, "Muscle3.9"),
os.path.join(prog_files, "Muscle")
] + sys.path
for folder in likely_dirs:
if os.path.isdir(folder):
if os.path.isfile(os.path.join(folder, "muscle.exe")):
muscle_exe = os.path.join(folder, "muscle.exe")
break
if muscle_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("muscle -version")
# Since "not found" may be in another language, try and be sure this is
# really the MUSCLE tool's output
if "not found" not in output and "MUSCLE" in output \
and "Edgar" in output:
muscle_exe = "muscle"
if not muscle_exe:
raise MissingExternalDependencyError(
"Install MUSCLE if you want to use the Bio.Align.Applications wrapper."
)
#################################################################
class MuscleApplication(unittest.TestCase):
"""Unit tests for Bio.Phylo.Applications wrappers."""
import sys
import os
import unittest
from Bio import Phylo
from Bio.Phylo.Applications import RaxmlCommandline
from Bio import MissingExternalDependencyError
raxml_exe = None
try:
from Bio._py3k import getoutput
output = getoutput("raxmlHPC -v")
if "not found" not in output and "This is RAxML" in output:
raxml_exe = "raxmlHPC"
except OSError:
# TODO: Use FileNotFoundError once we drop Python 2
pass
if not raxml_exe:
raise MissingExternalDependencyError(
"Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper."
)
# Example Phylip file with 4 aligned protein sequences
EX_PHYLIP = "Phylip/interlaced2.phy"
from Bio import MissingExternalDependencyError
from Bio import SeqIO
from Bio.Application import ApplicationError
from Bio.Motif.Applications import XXmotifCommandline
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
xxmotif_exe = None
if sys.platform == "win32":
# TODO
raise MissingExternalDependencyError("Testing this on Windows is not implemented yet")
else:
from Bio._py3k import getoutput
output = getoutput("XXmotif")
if output.find("== XXmotif version") != -1:
xxmotif_exe = "XXmotif"
if not xxmotif_exe:
raise MissingExternalDependencyError(
"Install XXmotif if you want to use XXmotif from Biopython.")
class XXmotifTestCase(unittest.TestCase):
def setUp(self):
self.out_dir = "xxmotif-temp"
self.files_to_clean = set()
def tearDown(self):
likely_exes = ["clustalw2.exe",
"clustalw.exe", "clustalw1.83.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)):
clustalw_exe = os.path.join(prog_files, folder, filename)
break
if clustalw_exe:
break
else:
from Bio._py3k import getoutput
# Note that clustalw 1.83 and clustalw 2.1 don't obey the --version
# command, but this does cause them to quit cleanly. Otherwise they prompt
# the user for input (causing a lock up).
output = getoutput("clustalw2 --version")
# Since "not found" may be in another language, try and be sure this is
# really the clustalw tool's output
if "not found" not in output and "CLUSTAL" in output \
and "Multiple Sequence Alignments" in output:
clustalw_exe = "clustalw2"
if not clustalw_exe:
output = getoutput("clustalw --version")
if "not found" not in output and "CLUSTAL" in output \
and "Multiple Sequence Alignments" in output:
clustalw_exe = "clustalw"
if not clustalw_exe:
raise MissingExternalDependencyError(
"Install clustalw or clustalw2 if you want to use it from Biopython.")
prog_files = os.environ["PROGRAMFILES"]
except KeyError:
prog_files = r"C:\Program Files"
likely_dirs = ["bwa", "bwa-0.6.2", ""]
likely_exes = ["bwa"]
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)):
bwa_exe = os.path.join(prog_files, folder, filename)
break
if bwa_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("bwa")
#Since "not found" may be in another language, try and be sure this is
#really the bwa tool's output
bwa_found = False
if "not found" not in output and "bwa" in output \
and "alignment via Burrows-Wheeler transformation" in output:
bwa_exe = "bwa"
if not bwa_exe:
raise MissingExternalDependencyError("Install bwa and correctly set"
" the file path to the program if"
" you want to use it from Biopython")
class BwaTestCase(unittest.TestCase):
import sys
import os
import unittest
import subprocess
from Bio import MissingExternalDependencyError
from Bio.Align.Applications import MafftCommandline
#Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
mafft_exe = None
if sys.platform=="win32":
raise MissingExternalDependencyError("Testing with MAFFT not implemented on Windows yet")
else:
from Bio._py3k import getoutput
output = getoutput("mafft -help")
if "not found" not in output and "MAFFT" in output:
mafft_exe = "mafft"
if not mafft_exe:
raise MissingExternalDependencyError(
"Install MAFFT if you want to use the Bio.Align.Applications wrapper.")
def check_mafft_version(mafft_exe):
child = subprocess.Popen("%s --help" % mafft_exe,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform!="win32"))
stdoutdata, stderrdata = child.communicate()
output = stdoutdata + "\n" + stderrdata
prog_files = r"C:\Program Files"
# By default tries C:\Program Files\samtools\samtools.exe
# or C:\Program Files\samtools.exe was chosen
likely_dirs = ["samtools", ""]
likely_exes = ["samtools.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)):
samtools_exe = os.path.join(prog_files, folder, filename)
break
if samtools_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("samtools")
#Since "not found" may be in another language, try and be sure this is
#really the samtools tool's output
if ("not found" not in output and
"samtools (Tools for alignments in the SAM format)" in output):
samtools_exe = "samtools"
if not samtools_exe:
raise MissingExternalDependencyError(
"""Install samtools and correctly set the file path to the program
if you want to use it from Biopython""")
class SamtoolsTestCase(unittest.TestCase):
"""Class for implementing Samtools test cases."""
# For Windows, PRANK just comes as a zip file which contains the
# prank.exe file which the user could put anywhere. We'll try a few
# sensible locations under Program Files... and then the full path.
likely_dirs = ["", # Current dir
prog_files,
os.path.join(prog_files, "Prank")] + sys.path
for folder in likely_dirs:
if os.path.isdir(folder):
if os.path.isfile(os.path.join(folder, "prank.exe")):
prank_exe = os.path.join(folder, "prank.exe")
break
if prank_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("prank")
if "not found" not in output and "prank" in output.lower():
prank_exe = "prank"
if not prank_exe:
raise MissingExternalDependencyError(
"Install PRANK if you want to use the Bio.Align.Applications wrapper.")
class PrankApplication(unittest.TestCase):
def setUp(self):
self.infile1 = "Fasta/fa01"
def tearDown(self):
"""
output.1.dnd output.1.fas output.1.xml output.2.dnd output.2.fas output.2.xml
import sys
import os
import unittest
from Bio._py3k import StringIO
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import ProbconsCommandline
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"
probcons_exe = None
if sys.platform == "win32":
raise MissingExternalDependencyError("PROBCONS not available on Windows")
else:
from Bio._py3k import getoutput
output = getoutput("probcons")
if "not found" not in output and "probcons" in output.lower():
probcons_exe = "probcons"
if not probcons_exe:
raise MissingExternalDependencyError(
"Install PROBCONS if you want to use the Bio.Align.Applications wrapper."
)
class ProbconsApplication(unittest.TestCase):
def setUp(self):
self.infile1 = "Fasta/fa01"
self.annotation_outfile = "Fasta/probcons_annot.out"
def tearDown(self):
import sys
import os
import unittest
from Bio import Phylo
from Bio.Phylo.Applications import PhymlCommandline
from Bio import MissingExternalDependencyError
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
phyml_exe = None
exe_name = "PhyML-3.1_win32.exe" if sys.platform == "win32" else "phyml"
from Bio._py3k import getoutput
try:
output = getoutput(exe_name + " --version")
if "not found" not in output and "20" in output:
phyml_exe = exe_name
except OSError:
# TODO: Use FileNotFoundError once we drop Python 2
# Python 2.6 or 2.7 on Windows XP:
# WindowsError: [Error 2] The system cannot find the file specified
# Python 3.3 or 3.4 on Windows XP:
# FileNotFoundError: [WinError 2] The system cannot find the file specified
pass
if not phyml_exe:
raise MissingExternalDependencyError(
"Install PhyML 3.0 if you want to use the Bio.Phylo.Applications wrapper.")
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")
from Bio import AlignIO
from Bio.Align.Applications import ClustalOmegaCommandline
from Bio.Application import ApplicationError
#################################################################
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
clustalo_exe = None
if sys.platform=="win32":
# TODO
raise MissingExternalDependencyError("Testing this on Windows not implemented yet")
else:
from Bio._py3k import getoutput
output = getoutput("clustalo --help")
if output.startswith("Clustal Omega"):
clustalo_exe = "clustalo"
if not clustalo_exe:
raise MissingExternalDependencyError(
"Install clustalo if you want to use Clustal Omega from Biopython.")
class ClustalOmegaTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
def tearDown(self):
for filename in self.files_to_clean:
#sensible locations under Program Files... and then the full path.
likely_dirs = [
"", # Current dir
prog_files,
os.path.join(prog_files, "Prank")
] + sys.path
for folder in likely_dirs:
if os.path.isdir(folder):
if os.path.isfile(os.path.join(folder, "prank.exe")):
prank_exe = os.path.join(folder, "prank.exe")
break
if prank_exe:
break
else:
from Bio._py3k import getoutput
output = getoutput("prank")
if "not found" not in output and "prank" in output.lower():
prank_exe = "prank"
if not prank_exe:
raise MissingExternalDependencyError(
"Install PRANK if you want to use the Bio.Align.Applications wrapper.")
class PrankApplication(unittest.TestCase):
def setUp(self):
self.infile1 = "Fasta/fa01"
def tearDown(self):
"""
output.1.dnd output.1.fas output.1.xml output.2.dnd output.2.fas output.2.xml
"""