コード例 #1
0
 def run(self, *args, **kwargs):
     start_worker(1)
     job = self.create_job(*args, **kwargs)
     jobq.put(job)
     return job.get_results()
コード例 #2
0
ファイル: test_raxml.py プロジェクト: SagesWang/pasta
import datetime
import logging
import os
import shutil, glob

from pasta.test import get_testing_configuration, data_source_path, TestLevel, is_test_enabled
from pasta import get_logger, log_exception
from pasta.alignment import Alignment, MultiLocusDataset
from pasta.scheduler import jobq, start_worker
from pasta.filemgr import TempFS
from pasta.usersettingclasses import StringUserSetting, IntUserSetting

_LOG = get_logger(__name__)

config = get_testing_configuration()
start_worker(1)

class TreeEstimatorTest(unittest.TestCase):
    def setUp(self):
        self.ts = TempFS()
        self.ts.create_top_level_temp(prefix='treeEstimatorTest', parent=os.curdir)
        self.filename = data_source_path('mafft.anolis.fasta')
        self.alignment = Alignment()
        self.alignment.read_filepath(data_source_path('mafft.anolis.fasta'),
                'FASTA')

    def tearDown(self):
        dir_list = self.ts.get_remaining_directories()
        for dir in dir_list:
            try:
                self.ts.remove_dir(dir)
コード例 #3
0
ファイル: test_aligners.py プロジェクト: hsnsa/pastaspark
import logging
import sys
import os

from pasta.test import get_testing_configuration, data_source_path, TestLevel, is_test_enabled

from pasta import get_logger
from pasta.alignment import Alignment
from pasta.scheduler import jobq, start_worker
from pasta.filemgr import TempFS

_LOG = get_logger(__name__)

config = get_testing_configuration()

start_worker(1)


class AlignerTest(unittest.TestCase):
    def setUp(self):
        self.ts = TempFS()
        self.ts.create_top_level_temp(prefix='alignerTesting',
                                      parent=os.curdir)

    def tearDown(self):
        dir_list = self.ts.get_remaining_directories()
        for dir in dir_list:
            self.ts.remove_dir(dir)

    def get_aligner(self, name):
        try:
コード例 #4
0
ファイル: tools.py プロジェクト: SagesWang/pasta
 def run(self, *args, **kwargs):
     start_worker(1)
     job = self.create_job(*args, **kwargs)
     jobq.put(job)
     return job.get_results()