import unittest
from Bio import SeqIO
from MEvoLib import MissingExtDependencyError
from MEvoLib import Inference
from MEvoLib._py3k import getoutput, viewkeys
#-------------------------------------------------------------------------------
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
fasttree_exe = None
if (sys.platform == 'win32'):
raise MissingExtDependencyError('Testing with FastTree not implemented on' \
' Windows yet')
else:
output = getoutput('fasttree')
if (('not found' not in output) and ('FastTree' in output)):
fasttree_exe = 'fasttree'
if (not fasttree_exe):
raise MissingExtDependencyError('Install FastTree if you want to use it ' \
'from MEvoLib.Inference.get_phylogeny().')
#-------------------------------------------------------------------------------
class InferenceTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
from Bio import SeqIO
from MEvoLib import MissingExtDependencyError
from MEvoLib import Inference
from MEvoLib._py3k import getoutput, viewkeys
#-------------------------------------------------------------------------------
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
raxml_exe = None
if ( sys.platform == 'win32' ) :
raise MissingExtDependencyError('Testing with RAxML not implemented on' \
' Windows yet')
else :
output = getoutput('raxml')
if ( ('not found' not in output) and ('RAxML' in output) ) :
raxml_exe = 'raxml'
if ( not raxml_exe ) :
raise MissingExtDependencyError('Install raxml if you want to use it from' \
' MEvoLib.Inference.get_phylogeny().')
#-------------------------------------------------------------------------------
class InferenceTestCase ( unittest.TestCase ) :
def setUp ( self ) :
self.files_to_clean = set()
import unittest
from Bio import SeqIO
from MEvoLib import MissingExtDependencyError
from MEvoLib import Align
from MEvoLib._py3k import getoutput, viewkeys, viewitems
#-------------------------------------------------------------------------------
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
mafft_exe = None
if (sys.platform == 'win32'):
raise MissingExtDependencyError('Testing with MAFFT not implemented on ' \
'Windows yet')
else:
output = getoutput('mafft --help')
if (('not found' not in output) and ('MAFFT' in output)):
mafft_exe = 'mafft'
if (not mafft_exe):
raise MissingExtDependencyError('Install MAFFT if you want to use it from' \
' MEvoLib.Align.get_alignment().')
#-------------------------------------------------------------------------------
class AlignTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
from Bio import Phylo
from MEvoLib import MissingExtDependencyError
from MEvoLib import PhyloAssemble
from MEvoLib._py3k import getoutput, viewkeys
#-------------------------------------------------------------------------------
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
consense_exe = None
if ( sys.platform == 'win32' ) :
raise MissingExtDependencyError('Testing with Consense not implemented on' \
' Windows yet')
else :
output = getoutput('type consense')
if ( 'not found' not in output ) :
consense_exe = 'consense'
if ( not consense_exe ) :
raise MissingExtDependencyError('Install Consense if you want to use it ' \
'from MEvoLib.PhyloAssemble.get_consensus_tree().')
#-------------------------------------------------------------------------------
class PhyloAssembleTestCase ( unittest.TestCase ) :
def setUp ( self ) :
self.files_to_clean = set()
import unittest
from Bio import SeqIO
from MEvoLib import MissingExtDependencyError
from MEvoLib import Cluster
from MEvoLib._py3k import getoutput, viewvalues
#-------------------------------------------------------------------------------
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
dcm3_exe = None
if (sys.platform == 'win32'):
raise MissingExtDependencyError('Testing with PRD not implemented on ' \
'Windows yet')
else:
output = getoutput('dcm')
if (('not found' not in output) and ('dcm' in output)):
dcm3_exe = 'dcm'
if (not dcm3_exe):
raise MissingExtDependencyError('Install DCM if you want to use it from' \
' MEvoLib.Cluster.get_subsets().')
#-------------------------------------------------------------------------------
class ClusterTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
import unittest
from Bio import SeqIO
from MEvoLib import MissingExtDependencyError
from MEvoLib import Align
from MEvoLib._py3k import getoutput, viewkeys, viewitems
#-------------------------------------------------------------------------------
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
muscle_exe = None
if (sys.platform == 'win32'):
raise MissingExtDependencyError('Testing with Muscle not implemented on ' \
'Windows yet')
else:
output = getoutput('muscle --help')
if (('not found' not in output) and ('MUSCLE' in output)):
muscle_exe = 'muscle'
if (not muscle_exe):
raise MissingExtDependencyError('Install Muscle if you want to use it ' \
'from MEvoLib.Align.get_alignment().')
#-------------------------------------------------------------------------------
class AlignTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
from MEvoLib import MissingExtDependencyError
from MEvoLib import Align
from MEvoLib._py3k import getoutput, viewkeys, viewitems
#-------------------------------------------------------------------------------
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
clustalo_exe = None
output = getoutput('clustalo --help')
if ( ('not found' not in output) and ('Clustal Omega' in output) ) :
clustalo_exe = 'clustalo'
if ( not clustalo_exe ) :
raise MissingExtDependencyError('Install Clustal Omega if you want to use' \
' it from MEvoLib.Align.get_alignment().')
#-------------------------------------------------------------------------------
class AlignTestCase ( unittest.TestCase ) :
def setUp ( self ) :
self.files_to_clean = set()
def tearDown ( self ) :
for filename in self.files_to_clean :
if ( os.path.isfile(filename) ) :
os.remove(filename)