class Tests(unittest.TestCase):
def setUp(self):
self.output_directory_path = os.path.join(my_path, 'test-decomposition-threaded')
self.decomposer = Decomposer()
self.decomposer.alignment = os.path.join(my_path, 'files/reads-noisy.fa')
self.decomposer.min_entropy = 0.3
self.decomposer.min_actual_abundance = 0
self.decomposer.min_substantive_abundance = 2
self.decomposer.skip_check_input_file = True
self.decomposer.number_of_discriminants = 1
self.decomposer.progress.verbose = False
self.decomposer.run.verbose = False
self.decomposer.skip_removing_outliers = False
self.decomposer.relocate_outliers = True
self.decomposer.skip_agglomerating_nodes = True
self.decomposer.threading = True
self.decomposer.output_directory = self.output_directory_path
def tearDown(self):
pass
def test_02_Decompose(self):
self.decomposer.decompose()
def test_02_Environment(self):
self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/reads-noisy-environment.txt'),
os.path.join(self.output_directory_path, 'ENVIRONMENT.txt')))
def test_03_MatrixPercent(self):
self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/reads-noisy-matrix-percent.txt'),
os.path.join(self.output_directory_path, 'MATRIX-PERCENT.txt')))
def test_99_CleanUp(self):
shutil.rmtree(self.output_directory_path)
class Tests(unittest.TestCase):
def setUp(self):
self.output_directory_path = os.path.join(my_path, 'test-decomposition-threaded')
self.decomposer = Decomposer()
self.decomposer.alignment = os.path.join(my_path, 'files/reads-noisy.fa')
self.decomposer.min_entropy = 0.3
self.decomposer.min_actual_abundance = 0
self.decomposer.min_substantive_abundance = 2
self.decomposer.number_of_discriminants = 1
self.decomposer.progress.verbose = False
self.decomposer.run.verbose = False
self.decomposer.skip_removing_outliers = False
self.decomposer.relocate_outliers = True
self.decomposer.skip_agglomerating_nodes = True
self.decomposer.threading = True
self.decomposer.output_directory = self.output_directory_path
def tearDown(self):
pass
def test_02_Decompose(self):
self.decomposer.decompose()
def test_02_Environment(self):
self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/reads-noisy-environment.txt'),
os.path.join(self.output_directory_path, 'ENVIRONMENT.txt')))
def test_03_MatrixPercent(self):
self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/reads-noisy-matrix-percent.txt'),
os.path.join(self.output_directory_path, 'MATRIX-PERCENT.txt')))
def test_99_CleanUp(self):
shutil.rmtree(self.output_directory_path)
class Tests(unittest.TestCase):
def setUp(self):
self.output_directory_path = os.path.join(my_path,
'test-decomposition')
self.decomposer = Decomposer()
self.decomposer.alignment = os.path.join(my_path,
'files/clone43-v6v4.fa')
self.decomposer.min_entropy = 0.2
self.decomposer.min_actual_abundance = 1
self.decomposer.min_substantive_abundance = 1
self.decomposer.skip_check_input_file = True
self.decomposer.number_of_discriminants = 3
self.decomposer.progress.verbose = False
self.decomposer.run.verbose = False
self.decomposer.skip_removing_outliers = True
self.decomposer.skip_agglomerating_nodes = True
self.decomposer.output_directory = self.output_directory_path
def tearDown(self):
pass
def test_01_PrefixGenerator(self):
prefix = self.decomposer.get_prefix()
self.assertTrue(prefix == 'm0.20-A1-M1-d3')
def test_02_Decompose(self):
self.decomposer.decompose()
self.assertTrue(self.decomposer.topology.nodes['root'].discriminants ==
[292, 296, 293])
self.assertTrue(
self.decomposer.topology.nodes['root'].entropy_tpls[0:5] == [(
292, 2.2031591775819033), (
296, 2.1539606786564707), (
293, 2.1279277605456857), (
298, 2.1170394670626229), (300,
2.107517097722345)])
self.assertTrue(len(self.decomposer.topology.nodes) == 54)
self.assertTrue(len(self.decomposer.topology.final_nodes) == 43)
def test_03_Environment(self):
self.assertTrue(
files_are_the_same(
os.path.join(my_path, 'files/clone43-v6v4-environment.txt'),
os.path.join(self.output_directory_path, 'ENVIRONMENT.txt')))
def test_04_MatrixPercent(self):
self.assertTrue(
files_are_the_same(
os.path.join(my_path, 'files/clone43-v6v4-matrix-percent.txt'),
os.path.join(self.output_directory_path,
'MATRIX-PERCENT.txt')))
def test_99_CleanUp(self):
shutil.rmtree(self.output_directory_path)
def setUp(self):
self.output_directory_path = os.path.join(my_path,
'test-decomposition')
self.decomposer = Decomposer()
self.decomposer.alignment = os.path.join(my_path,
'files/clone43-v6v4.fa')
self.decomposer.min_entropy = 0.2
self.decomposer.min_actual_abundance = 1
self.decomposer.min_substantive_abundance = 0
self.decomposer.number_of_discriminants = 3
self.decomposer.progress.verbose = False
self.decomposer.run.verbose = False
self.decomposer.skip_removing_outliers = True
self.decomposer.skip_agglomerating_nodes = True
self.decomposer.output_directory = self.output_directory_path
def setUp(self):
self.output_directory_path = os.path.join(my_path, 'test-decomposition-threaded')
self.decomposer = Decomposer()
self.decomposer.alignment = os.path.join(my_path, 'files/reads-noisy.fa')
self.decomposer.min_entropy = 0.3
self.decomposer.min_actual_abundance = 0
self.decomposer.min_substantive_abundance = 2
self.decomposer.skip_check_input_file = True
self.decomposer.number_of_discriminants = 1
self.decomposer.progress.verbose = False
self.decomposer.run.verbose = False
self.decomposer.skip_removing_outliers = False
self.decomposer.relocate_outliers = True
self.decomposer.skip_agglomerating_nodes = True
self.decomposer.threading = True
self.decomposer.output_directory = self.output_directory_path
class Tests(unittest.TestCase):
def setUp(self):
self.output_directory_path = os.path.join(my_path, 'test-decomposition')
self.decomposer = Decomposer()
self.decomposer.alignment = os.path.join(my_path, 'files/clone43-v6v4.fa')
self.decomposer.min_entropy = 0.2
self.decomposer.min_actual_abundance = 1
self.decomposer.min_substantive_abundance = 1
self.decomposer.skip_check_input_file = True
self.decomposer.number_of_discriminants = 3
self.decomposer.progress.verbose = False
self.decomposer.run.verbose = False
self.decomposer.skip_removing_outliers = True
self.decomposer.skip_agglomerating_nodes = True
self.decomposer.output_directory = self.output_directory_path
def tearDown(self):
pass
def test_01_PrefixGenerator(self):
prefix = self.decomposer.get_prefix()
self.assertTrue(prefix == 'm0.20-A1-M1-d3')
def test_02_Decompose(self):
self.decomposer.decompose()
self.assertTrue(self.decomposer.topology.nodes['root'].discriminants == [292, 296, 293])
self.assertTrue(self.decomposer.topology.nodes['root'].entropy_tpls[0:5] == [(292, 2.2031591775819033), (296, 2.1539606786564707), (293, 2.1279277605456857), (298, 2.1170394670626229), (300, 2.107517097722345)])
self.assertTrue(len(self.decomposer.topology.nodes) == 54)
self.assertTrue(len(self.decomposer.topology.final_nodes) == 43)
def test_03_Environment(self):
self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/clone43-v6v4-environment.txt'),
os.path.join(self.output_directory_path, 'ENVIRONMENT.txt')))
def test_04_MatrixPercent(self):
self.assertTrue(files_are_the_same(os.path.join(my_path, 'files/clone43-v6v4-matrix-percent.txt'),
os.path.join(self.output_directory_path, 'MATRIX-PERCENT.txt')))
def test_99_CleanUp(self):
shutil.rmtree(self.output_directory_path)
def setUp(self):
self.output_directory_path = os.path.join(my_path, 'test-decomposition')
self.decomposer = Decomposer()
self.decomposer.alignment = os.path.join(my_path, 'files/clone43-v6v4.fa')
self.decomposer.min_entropy = 0.2
self.decomposer.min_actual_abundance = 1
self.decomposer.min_substantive_abundance = 0
self.decomposer.number_of_discriminants = 3
self.decomposer.progress.verbose = False
self.decomposer.run.verbose = False
self.decomposer.skip_removing_outliers = True
self.decomposer.skip_agglomerating_nodes = True
self.decomposer.output_directory = self.output_directory_path
def setUp(self):
self.output_directory_path = os.path.join(my_path, 'test-decomposition-threaded')
self.decomposer = Decomposer()
self.decomposer.alignment = os.path.join(my_path, 'files/reads-noisy.fa')
self.decomposer.min_entropy = 0.3
self.decomposer.min_actual_abundance = 0
self.decomposer.min_substantive_abundance = 2
self.decomposer.number_of_discriminants = 1
self.decomposer.progress.verbose = False
self.decomposer.run.verbose = False
self.decomposer.skip_removing_outliers = False
self.decomposer.relocate_outliers = True
self.decomposer.skip_agglomerating_nodes = True
self.decomposer.threading = True
self.decomposer.output_directory = self.output_directory_path
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# Please read the COPYING file.
import os
import sys
from Oligotyping.lib.decomposer import Decomposer
from Oligotyping.utils.utils import ConfigError
from Oligotyping.utils import parsers
# med_out_dir = '/Users/humebc/phylogenetic_software/med_hume'
# path_to_file = '/Users/humebc/phylogenetic_software/med_hume/test_fasta.fasta'
# ['-M', '4', '--skip-gexf-files', '--skip-gen-figures', '--skip-gen-html', '--skip-check-input', '-o', med_out_dir,
# path_to_file]
parser = parsers.decomposer()
decomposer = Decomposer(parser.parse_args())
try:
decomposer.decompose()
except ConfigError as e:
print(e)
sys.exit(-1)
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# Please read the COPYING file.
import os
import sys
import cPickle
from Oligotyping.lib.decomposer import Decomposer
from Oligotyping.utils.utils import get_samples_dict_from_environment_file
runinfo = cPickle.load(open(sys.argv[1]))
sample_mapping = sys.argv[2]
decomposer = Decomposer()
decomposer.matrix_percent_file_path = runinfo['matrix_percent_file_path']
decomposer.matrix_count_file_path = runinfo['matrix_count_file_path']
decomposer.tmp_directory = runinfo['tmp_directory']
decomposer.output_directory = runinfo['output_directory']
decomposer.figures_directory = os.path.join(os.path.dirname(runinfo['figures_directory']), 'FIGURES')
if not os.path.exists(decomposer.tmp_directory):
os.makedirs(decomposer.tmp_directory)
decomposer.sample_mapping = sample_mapping
decomposer._init_logger('exclusive_figures.log')
decomposer.samples_dict = get_samples_dict_from_environment_file(runinfo['environment_file_path'])
decomposer.samples = sorted(decomposer.samples_dict.keys())
decomposer._generate_exclusive_figures()
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# Please read the COPYING file.
import os
import sys
import cPickle
from Oligotyping.lib.decomposer import Decomposer
from Oligotyping.utils.utils import get_samples_dict_from_environment_file
runinfo = cPickle.load(open(sys.argv[1]))
sample_mapping = sys.argv[2]
decomposer = Decomposer()
decomposer.matrix_percent_file_path = runinfo['matrix_percent_file_path']
decomposer.matrix_count_file_path = runinfo['matrix_count_file_path']
decomposer.tmp_directory = runinfo['tmp_directory']
decomposer.output_directory = runinfo['output_directory']
decomposer.figures_directory = os.path.join(
os.path.dirname(runinfo['figures_directory']), 'FIGURES')
if not os.path.exists(decomposer.tmp_directory):
os.makedirs(decomposer.tmp_directory)
decomposer.sample_mapping = sample_mapping
decomposer._init_logger('exclusive_figures.log')
decomposer.samples_dict = get_samples_dict_from_environment_file(
runinfo['environment_file_path'])
decomposer.samples = sorted(decomposer.samples_dict.keys())