Python getoutput 예제들

예제 #1

파일: test_Cluster_PRD.py 프로젝트: JAlvarezJarreta/MEvoLib

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()

    def tearDown(self):
        for filename in self.files_to_clean:

예제 #2

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()

    def tearDown(self):
        for filename in self.files_to_clean:

예제 #3

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()

예제 #4

파일: test_Align_Mafft.py 프로젝트: JAlvarezJarreta/MEvoLib

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()

    def tearDown(self):
        for filename in self.files_to_clean:

예제 #5

파일: test_Cluster_Genes.py 프로젝트: JAlvarezJarreta/MEvoLib

from Bio import SeqIO

from MEvoLib import MissingExtDependencyError
from MEvoLib import Cluster
from MEvoLib._py3k import getoutput, viewvalues, viewitems


# -------------------------------------------------------------------------------

# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"

mafft_exe = None
if sys.platform != "win32":
    output = getoutput("mafft --help")
    if ("not found" not in output) and ("MAFFT" in output):
        mafft_exe = "mafft"


# -------------------------------------------------------------------------------


class ClusterTestCase(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)

예제 #6

파일: test_PhyloAssemble_Consense.py 프로젝트: JAlvarezJarreta/MEvoLib

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()

예제 #7

파일: test_Inference_FastTree.py 프로젝트: JAlvarezJarreta/MEvoLib

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()

예제 #8

파일: test_Cluster_PRD.py 프로젝트: JAlvarezJarreta/MEvoLib

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()

    def tearDown(self):
        for filename in self.files_to_clean:

예제 #9

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()

    def tearDown(self):
        for filename in self.files_to_clean:

예제 #10

파일: test_Align_Muscle.py 프로젝트: JAlvarezJarreta/MEvoLib

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()

예제 #11

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'

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()

예제 #12

파일: test_Align_Mafft.py 프로젝트: JAlvarezJarreta/MEvoLib

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()