/
test_util.py
572 lines (502 loc) · 25.7 KB
/
test_util.py
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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, emperor development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.md, distributed with this software.
# ----------------------------------------------------------------------------
from __future__ import division
from unittest import TestCase, main
from os.path import exists, join
from shutil import rmtree
from tempfile import gettempdir
import pandas as pd
import warnings
from numpy import array
from numpy.testing import assert_almost_equal
from emperor.util import (
preprocess_coords_file,
nbinstall, validate_and_process_custom_axes,
resolve_stable_url, EmperorWarning)
warnings.simplefilter('always', category=EmperorWarning)
class TopLevelTests(TestCase):
def setUp(self):
self.files_to_delete = []
self.mapping_file_data = MAPPING_FILE_DATA
self.mapping_file_headers = ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment',
'DOB', 'Description']
self.valid_columns = ['Treatment', 'DOB']
self.support_files_filename = gettempdir()
self.support_files_filename_spaces = join(
gettempdir(), 'Directory With Spaces/AndNoSpaces')
# data for the custom axes, contains columns that are gradients
self.mapping_file_data_gradient = MAPPING_FILE_DATA_GRADIENT
self.mapping_file_headers_gradient = ['SampleID', 'Treatment', 'Time',
'Weight', 'Description']
self.coords_header = ['PC.355', 'PC.635', 'PC.636', 'PC.354']
self.coords_data = COORDS_DATA
self.coords_eigenvalues = array([1, 2, 3, 4])
self.coords_pct = array([40, 30, 20, 10])
# jackknifed test data
self.jk_mapping_file_headers = ['SampleID', 'C2', 'C3', 'C4']
self.jk_mapping_file_data = [['1', 'a', 'b', 'c'],
['2', 'd', 'e', 'f'],
['3', 'g', 'h', 'i']]
self.jk_coords_header = [['1', '2', '3'], ['1', '2', '3'],
['1', '2', '3'], ['1', '2', '3']]
self.jk_coords_data = [
array([[1.2, 0.1, -1.2], [-2.5, -4.0, 4.5]]),
array([[-1.4, 0.05, 1.3], [2.6, 4.1, -4.7]]),
array([[-1.5, 0.05, 1.6], [2.4, 4.0, -4.8]]),
array([[-1.5, 0.05, 1.6], [2.4, 4.0, -4.8]])]
self.jk_coords_eigenvalues = [
array([0.80, .11, 0.09]),
array([0.76, .20, 0.04]),
array([0.84, .14, 0.02]),
array([0.84, .11, 0.05])]
self.jk_coords_pcts = [
array([0.80, .10, 0.10]),
array([0.76, .21, 0.03]),
array([0.84, .11, 0.05]),
array([0.84, .15, 0.01])]
self.jk_mapping_file_data_gradient = MAPPING_FILE_DATA_GRADIENT
self.jk_mapping_file_headers_gradient = ['SampleID', 'Treatment',
'Time', 'Weight',
'Description']
self.jk_coords_header_gradient = [
['PC.354', 'PC.355', 'PC.635', 'PC.636'],
['PC.354', 'PC.355', 'PC.635', 'PC.636'],
['PC.354', 'PC.355', 'PC.635', 'PC.636'],
['PC.354', 'PC.355', 'PC.635', 'PC.636']]
self.jk_coords_data_gradient = [
array([[1.2, 0.1, -1.2, 1.1],
[-2.5, -4.0, 4.5, 0.3],
[.5, -0.4, 3.5, 1.001],
[0.67, 0.23, 1.01, 2.2]]),
array([[1.2, 1, -0.2, 0.1],
[-2.5, -4.0, 4.5, 3.2],
[.5, -0.4, 3.5, 1.00],
[0.57, 0.27, 0.95, 2.1]]),
array([[1.0, 1, -1.2, 1.1],
[-2.1, -2.0, 3.5, 0.3],
[.5, 3, 3.5, 2],
[0.60, 0.33, 1.3, 2.0]]),
array([[1.2, 0.1, -1.2, 1.1],
[-2.5, -4.0, 4.5, 0.3],
[.5, -0.4, 3.5, 1.001],
[0.69, 0.20, 1.01, 2.2]])]
self.jk_coords_eigenvalues_gradient = [
array([0.80, .11, 0.09, 0.0]),
array([0.76, .20, 0.04, 0.0]),
array([0.84, .14, 0.02, 0.0]),
array([0.84, .11, 0.05, 0.0])]
self.jk_coords_pcts_gradient = [
array([0.80, .10, 0.10, 0.0]),
array([0.76, .21, 0.03, 0.0]),
array([0.84, .11, 0.05, 0.0]),
array([0.84, .15, 0.01, 0])]
self.broken_mapping_file_data = BROKEN_MAPPING_FILE
self.broken_mapping_file_data_2_values = BROKEN_MAPPING_FILE_2_VALUES
def tearDown(self):
for f in self.files_to_delete:
rmtree(f)
def test_preprocess_coords_file(self):
"""Check correct processing is applied to the coords"""
# case with custom axes
out_coords_header, out_coords_data, out_eigenvals, out_pcts,\
out_coords_low, out_coords_high, o_clones = preprocess_coords_file(
self.coords_header, self.coords_data, self.coords_eigenvalues,
self.coords_pct, self.mapping_file_headers_gradient,
self.mapping_file_data_gradient, ['Time'])
expected_coords_data = array(
[[0.03333333, -0.2, -0.1, 0.06, -0.06],
[0.03333333, -0.3, 0.04, -0.1, 0.15],
[0.2, 0.1, -0.1, -0.2, 0.08],
[-0.3, 0.04, -0.01, 0.06, -0.34]])
self.assertEqual(out_coords_header, self.coords_header)
self.assertEqual(out_coords_high, None)
self.assertEqual(out_coords_low, None)
assert_almost_equal(self.coords_eigenvalues, array([1, 2, 3, 4]))
assert_almost_equal(self.coords_pct, array([40, 30, 20, 10]))
self.assertEqual(o_clones, 0)
# check each individual value because currently cogent assertEquals
# fails when comparing the whole matrix at once
for out_el, exp_el in zip(out_coords_data, expected_coords_data):
for out_el_sub, exp_el_sub in zip(out_el, exp_el):
self.assertAlmostEqual(out_el_sub, exp_el_sub)
# case for jackknifing, based on qiime/tests/test_util.summarize_pcoas
out_coords_header, out_coords_data, out_eigenvals, out_pcts,\
out_coords_low, out_coords_high, o_clones = preprocess_coords_file(
self.jk_coords_header, self.jk_coords_data,
self.jk_coords_eigenvalues, self.jk_coords_pcts,
self.jk_mapping_file_headers, self.jk_mapping_file_data,
jackknifing_method='sdev', pct_variation_below_one=True)
self.assertEqual(out_coords_header, ['1', '2', '3'])
assert_almost_equal(out_coords_data, array([[1.4, -0.0125, -1.425],
[-2.475, -4.025, 4.7]]))
assert_almost_equal(out_eigenvals, array([0.81, 0.14, 0.05]))
assert_almost_equal(out_pcts, array([0.8, 0.1, 0.1]))
self.assertEqual(o_clones, 0)
# test the coords are working fine
assert_almost_equal(out_coords_low,
array([[-0.07071068, -0.0375, -0.10307764],
[-0.04787136, -0.025, -0.07071068]]))
assert_almost_equal(out_coords_high,
array([[0.07071068, 0.0375, 0.10307764],
[0.04787136, 0.025, 0.07071068]]))
# test custom axes and jackknifed plots
out_coords_header, out_coords_data, out_eigenvals, out_pcts,\
out_coords_low, out_coords_high, o_clones = preprocess_coords_file(
self.jk_coords_header_gradient, self.jk_coords_data_gradient,
self.jk_coords_eigenvalues_gradient,
self.jk_coords_pcts_gradient,
self.jk_mapping_file_headers_gradient,
self.jk_mapping_file_data_gradient, custom_axes=['Time'],
jackknifing_method='sdev', pct_variation_below_one=True)
self.assertEqual(out_coords_header,
['PC.354', 'PC.355', 'PC.635', 'PC.636'])
assert_almost_equal(out_coords_data,
array([[-2.4, 1.15, 0.55, -0.95, 0.85],
[0.73333333, -2.4, -3.5, 4.25, 1.025],
[0.73333333, 0.5, 0.45, 3.5, 1.2505],
[2.3, 0.6325, 0.2575, 1.0675, 2.125]]))
assert_almost_equal(out_eigenvals, array([0.81, 0.14, 0.05, 0.]))
assert_almost_equal(out_pcts, array([0.8, 0.1, 0.1, 0.]))
# test the coords are working fine
assert_almost_equal(
out_coords_low,
array([[0., -0.05, -0.25980762, -0.25, -0.25],
[0., -0.1, -0.5, -0.25, -0.725],
[0., -0., -0.85, -0., -0.24983344],
[0., -0.0283945, -0.02809953, -0.07877976, -0.04787136]]))
assert_almost_equal(
out_coords_high,
array([[1.00000000e-05, 5.0000000e-02, 2.59807621e-01,
2.50000000e-01, 2.50000000e-01],
[1.00000000e-05, 1.0000000e-01, 5.00000000e-01,
2.50000000e-01, 7.25000000e-01],
[1.00000000e-05, 0.0, 8.50000000e-01, 0.00000000e+00,
2.49833445e-01],
[1.00000000e-05, 2.83945417e-02, 2.80995255e-02,
7.87797563e-02, 4.78713554e-02]]))
self.assertEqual(o_clones, 0)
# test that pct_variation_below_one is working
out_coords_header, out_coords_data, out_eigenvals, out_pcts,\
out_coords_low, out_coords_high, o_clones = preprocess_coords_file(
self.jk_coords_header_gradient, self.jk_coords_data_gradient,
self.jk_coords_eigenvalues_gradient,
self.jk_coords_pcts_gradient,
self.jk_mapping_file_headers_gradient,
self.jk_mapping_file_data_gradient, custom_axes=['Time'],
jackknifing_method='sdev', pct_variation_below_one=False)
self.assertEqual(out_coords_header,
['PC.354', 'PC.355', 'PC.635', 'PC.636'])
assert_almost_equal(
out_coords_data,
array([[-2.4, 1.15, 0.55, -0.95, 0.85],
[0.73333333, -2.4, -3.5, 4.25, 1.025],
[0.73333333, 0.5, 0.45, 3.5, 1.2505],
[2.3, 0.6325, 0.2575, 1.0675, 2.125]]))
assert_almost_equal(out_eigenvals, array([0.81, 0.14, 0.05, 0.]))
assert_almost_equal(out_pcts, array([80, 10, 10, 0]))
def test_preprocess_coords_file_comparison(self):
"""Check the cases for comparisons plots and the special usages"""
# shouldn't allow a comparison computation with only one file
self.assertRaises(
AssertionError, preprocess_coords_file,
self.coords_header, self.coords_data, self.coords_eigenvalues,
self.coords_pct, self.mapping_file_headers_gradient,
self.mapping_file_data_gradient, None, None, True)
out_coords_header, out_coords_data, out_eigenvals, out_pcts,\
out_coords_low, out_coords_high, o_clones = preprocess_coords_file(
self.jk_coords_header, self.jk_coords_data,
self.jk_coords_eigenvalues, self.jk_coords_pcts,
self.jk_mapping_file_headers, self.jk_mapping_file_data,
is_comparison=True, pct_variation_below_one=True)
self.assertEqual(out_coords_header,
['1_0', '2_0', '3_0', '1_1', '2_1', '3_1', '1_2',
'2_2', '3_2', '1_3', '2_3', '3_3'])
assert_almost_equal(
out_coords_data,
array([[1.2, 0.1, -1.2],
[-2.5, -4., 4.5],
[-1.4, 0.05, 1.3],
[2.6, 4.1, -4.7],
[-1.5, 0.05, 1.6],
[2.4, 4., -4.8],
[-1.5, 0.05, 1.6],
[2.4, 4., -4.8]]))
assert_almost_equal(out_eigenvals, self.jk_coords_eigenvalues[0])
assert_almost_equal(out_pcts, self.jk_coords_pcts[0])
self.assertEqual(out_coords_low, None)
self.assertEqual(out_coords_high, None)
self.assertEqual(o_clones, 4)
def test_nbinstall(self):
temp_dir = gettempdir()
target_path = join(temp_dir, 'share/jupyter/nbextensions/emperor/'
'support_files')
# remove the whole tree
self.files_to_delete.append(join(temp_dir, 'share'))
nbinstall(prefix=temp_dir, user=None)
self.assertTrue(exists(target_path))
def test_custom_axes(self):
columns = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Treatment', 'DOB', 'Description']
mf = pd.DataFrame(data=MAPPING_FILE_DATA, columns=columns)
obs = validate_and_process_custom_axes(mf, ['DOB'])
exp = pd.DataFrame(data=MAPPING_FILE_DATA_CONVERTED, columns=columns)
pd.util.testing.assert_frame_equal(obs, exp)
def test_custom_axes_non_existent_names(self):
columns = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Treatment', 'DOB', 'Description']
mf = pd.DataFrame(data=MAPPING_FILE_DATA, columns=columns)
with self.assertRaises(KeyError):
validate_and_process_custom_axes(mf, [':L'])
with self.assertRaises(KeyError):
validate_and_process_custom_axes(mf, ['D0B'])
def test_custom_axes_non_numeric_values(self):
columns = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Treatment', 'DOB', 'Description']
mf = pd.DataFrame(data=MAPPING_FILE_DATA, columns=columns)
with self.assertRaises(ValueError):
validate_and_process_custom_axes(mf, ['Treatment'])
with self.assertRaises(ValueError):
validate_and_process_custom_axes(mf, ['SampleID'])
def test_custom_axes_non_numeric_values_mixed(self):
columns = ['SampleID', 'huey', 'dewey', 'louie', 'Description']
mf = pd.DataFrame(data=BROKEN_MAPPING_FILE, columns=columns)
with self.assertRaises(ValueError):
validate_and_process_custom_axes(mf, ['louie'])
with self.assertRaises(ValueError):
validate_and_process_custom_axes(mf, ['louie', 'dewey'])
def test_resolve_stable_url_release(self):
# we test that no warnings are raised
url = 'https://github.com/biocore/emperor@%s/emperor/support_files'
with warnings.catch_warnings(record=True) as w:
obs = resolve_stable_url('1.0.0b7', url)
self.assertTrue(len(w) == 0)
self.assertEqual(obs, url % '1.0.0-beta.7')
def test_resolve_stable_url_release_check_warning(self):
url = 'https://github.com/biocore/emperor@%s/emperor/support_files'
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
obs = resolve_stable_url('1.0.0b7.dev', url)
self.assertTrue(len(w) == 1)
self.assertTrue(issubclass(w[-1].category, EmperorWarning))
self.assertEqual(obs, url % '1.0.0-beta.7')
def test_resolve_stable_url_release_number_check_warning(self):
url = 'https://github.com/biocore/emperor@%s/emperor/support_files'
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
obs = resolve_stable_url('1.0.0b7.dev0', url)
self.assertTrue(len(w) == 1)
self.assertTrue(issubclass(w[-1].category, EmperorWarning))
self.assertEqual(obs, url % '1.0.0-beta.7')
MAPPING_FILE_DATA = [
['PC.354', 'AGCACGAGCCTA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218',
'Control_mouse_I.D._354'],
['PC.355', 'AACTCGTCGATG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218',
'Control_mouse_I.D._355'],
['PC.356', 'ACAGACCACTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126',
'Control_mouse_I.D._356'],
['PC.481', 'ACCAGCGACTAG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20070314',
'Control_mouse_I.D._481'],
['PC.593', 'AGCAGCACTTGT', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210',
'Control_mouse_I.D._593'],
['PC.607', 'AACTGTGCGTAC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112',
'Fasting_mouse_I.D._607'],
['PC.634', 'ACAGAGTCGGCT', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116',
'Fasting_mouse_I.D._634'],
['PC.635', 'ACCGCAGAGTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116',
'Fasting_mouse_I.D._635'],
['PC.636', 'ACGGTGAGTGTC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116',
'Fasting_mouse_I.D._636']]
MAPPING_FILE_DATA_CONVERTED = [
['PC.354', 'AGCACGAGCCTA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20061218,
'Control_mouse_I.D._354'],
['PC.355', 'AACTCGTCGATG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20061218,
'Control_mouse_I.D._355'],
['PC.356', 'ACAGACCACTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20061126,
'Control_mouse_I.D._356'],
['PC.481', 'ACCAGCGACTAG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20070314,
'Control_mouse_I.D._481'],
['PC.593', 'AGCAGCACTTGT', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20071210,
'Control_mouse_I.D._593'],
['PC.607', 'AACTGTGCGTAC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', 20071112,
'Fasting_mouse_I.D._607'],
['PC.634', 'ACAGAGTCGGCT', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', 20080116,
'Fasting_mouse_I.D._634'],
['PC.635', 'ACCGCAGAGTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', 20080116,
'Fasting_mouse_I.D._635'],
['PC.636', 'ACGGTGAGTGTC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', 20080116,
'Fasting_mouse_I.D._636']]
PRE_PROCESS_A = [
['PC.354', 'AGCACGAGCCTA', 'Control', '20061218'],
['PC.355', 'AACTCGTCGATG', 'Control', '20061218'],
['PC.356', 'ACAGACCACTCA', 'Control', '20061126'],
['PC.481', 'ACCAGCGACTAG', 'Control', '20070314'],
['PC.593', 'AGCAGCACTTGT', 'Control', '20071210'],
['PC.607', 'AACTGTGCGTAC', 'Fast', '20071112'],
['PC.634', 'ACAGAGTCGGCT', 'Fast', '20080116'],
['PC.635', 'ACCGCAGAGTCA', 'Fast', '20080116'],
['PC.636', 'ACGGTGAGTGTC', 'Fast', '20080116']]
PRE_PROCESS_B = [
['PC.354', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._354'],
['PC.355', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._355'],
['PC.356', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._356'],
['PC.481', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._481'],
['PC.593', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._593'],
['PC.607', 'YATGCTGCCTCCCGTAGGAGT', 'Fasting_mouse_I.D._607'],
['PC.634', 'YATGCTGCCTCCCGTAGGAGT', 'Fasting_mouse_I.D._634'],
['PC.635', 'YATGCTGCCTCCCGTAGGAGT', 'Fasting_mouse_I.D._635'],
['PC.636', 'YATGCTGCCTCCCGTAGGAGT', 'Fasting_mouse_I.D._636']]
MAPPING_FILE_DATA_CAT_A = [
['PC.354', 'Control', '20061218', 'Control20061218'],
['PC.355', 'Control', '20061218', 'Control20061218'],
['PC.356', 'Control', '20061126', 'Control20061126'],
['PC.481', 'Control', '20070314', 'Control20070314'],
['PC.593', 'Control', '20071210', 'Control20071210'],
['PC.607', 'Fast', '20071112', 'Fast20071112'],
['PC.634', 'Fast', '20080116', 'Fast20080116'],
['PC.635', 'Fast', '20080116', 'Fast20080116'],
['PC.636', 'Fast', '20080116', 'Fast20080116']]
MAPPING_FILE_DATA_CAT_B = [
['PC.354', 'Control', '20061218', '20061218Control'],
['PC.355', 'Control', '20061218', '20061218Control'],
['PC.356', 'Control', '20061126', '20061126Control'],
['PC.481', 'Control', '20070314', '20070314Control'],
['PC.593', 'Control', '20071210', '20071210Control'],
['PC.607', 'Fast', '20071112', '20071112Fast'],
['PC.634', 'Fast', '20080116', '20080116Fast'],
['PC.635', 'Fast', '20080116', '20080116Fast'],
['PC.636', 'Fast', '20080116', '20080116Fast']]
MAPPING_FILE_DATA_CAT_C = [
['PC.354', 'Control'], ['PC.355', 'Control'], ['PC.356', 'Control'],
['PC.481', 'Control'], ['PC.593', 'Control'], ['PC.607', 'Fast'],
['PC.634', 'Fast'], ['PC.635', 'Fast'], ['PC.636', 'Fast']]
MAPPING_FILE_DATA_CAT_D = [
['PC.354', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218'],
['PC.355', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218'],
['PC.356', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126'],
['PC.481', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20070314'],
['PC.593', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210'],
['PC.607', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112'],
['PC.634', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116'],
['PC.635', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116'],
['PC.636', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116']]
MAPPING_FILE_DATA_CAT_E = [
['PC.354', 'AGCACGAGCCTA', 'Control', '20061218',
'Control_mouse_I.D._354'],
['PC.355', 'AACTCGTCGATG', 'Control', '20061218',
'Control_mouse_I.D._355'],
['PC.356', 'ACAGACCACTCA', 'Control', '20061126',
'Control_mouse_I.D._356'],
['PC.481', 'ACCAGCGACTAG', 'Control', '20070314',
'Control_mouse_I.D._481'],
['PC.593', 'AGCAGCACTTGT', 'Control', '20071210',
'Control_mouse_I.D._593'],
['PC.607', 'AACTGTGCGTAC', 'Fast', '20071112', 'Fasting_mouse_I.D._607'],
['PC.634', 'ACAGAGTCGGCT', 'Fast', '20080116', 'Fasting_mouse_I.D._634'],
['PC.635', 'ACCGCAGAGTCA', 'Fast', '20080116', 'Fasting_mouse_I.D._635'],
['PC.636', 'ACGGTGAGTGTC', 'Fast', '20080116', 'Fasting_mouse_I.D._636']]
MAPPING_FILE_DATA_CAT_F = [
['PC.354', 'Control', 'Control20061218'],
['PC.355', 'Control', 'Control20061218'],
['PC.356', 'Control', 'Control20061126'],
['PC.481', 'Control', 'Control20070314'],
['PC.593', 'Control', 'Control20071210'],
['PC.607', 'Fast', 'Fast20071112'],
['PC.634', 'Fast', 'Fast20080116'],
['PC.635', 'Fast', 'Fast20080116'],
['PC.636', 'Fast', 'Fast20080116']]
MAPPING_FILE_DATA_CAT_G = [
['PC.354', 'AGCACGAGCCTA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218',
'Control_mouse_I.D._354'],
['PC.355', 'AACTCGTCGATG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218',
'Control_mouse_I.D._355'],
['PC.356', 'ACAGACCACTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126',
'Control_mouse_I.D._356'],
['PC.481', 'ACCAGCGACTAG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20070314',
'Control_mouse_I.D._481'],
['PC.593', 'AGCAGCACTTGT', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210',
'Control_mouse_I.D._593'],
['PC.607', 'AACTGTGCGTAC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112',
'Fasting_mouse_I.D._607'],
['PC.634', 'ACAGAGTCGGCT', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116',
'Fasting_mouse_I.D._634'],
['PC.635', 'ACCGCAGAGTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116',
'Fasting_mouse_I.D._635'],
['PC.636', 'ACGGTGAGTGTC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116',
'Fasting_mouse_I.D._636']]
MAPPING_FILE_DATA_CAT_H = [
['PC.354', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218'],
['PC.355', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218'],
['PC.356', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126'],
['PC.481', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20070314'],
['PC.593', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210'],
['PC.607', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112'],
['PC.634', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116'],
['PC.635', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116'],
['PC.636', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116']]
MAPPING_FILE_DATA_GRADIENT = [
['PC.354', 'Control', '3', '40', 'Control20061218'],
['PC.355', 'Control', '9', '44', 'Control20061218'],
['PC.635', 'Fast', '9', '44', 'Fast20080116'],
['PC.636', 'Fast', '12', '37.22', 'Fast20080116']]
MAPPING_FILE_DATA_DUPLICATED = [
['PC.354_0', 'Control', '20061218'],
['PC.355_0', 'Control', '20061218'],
['PC.356_0', 'Control', '20061126'],
['PC.481_0', 'Control', '20070314'],
['PC.593_0', 'Control', '20071210'],
['PC.607_0', 'Fast', '20071112'],
['PC.634_0', 'Fast', '20080116'],
['PC.635_0', 'Fast', '20080116'],
['PC.636_0', 'Fast', '20080116'],
['PC.354_1', 'Control', '20061218'],
['PC.355_1', 'Control', '20061218'],
['PC.356_1', 'Control', '20061126'],
['PC.481_1', 'Control', '20070314'],
['PC.593_1', 'Control', '20071210'],
['PC.607_1', 'Fast', '20071112'],
['PC.634_1', 'Fast', '20080116'],
['PC.635_1', 'Fast', '20080116'],
['PC.636_1', 'Fast', '20080116'],
['PC.354_2', 'Control', '20061218'],
['PC.355_2', 'Control', '20061218'],
['PC.356_2', 'Control', '20061126'],
['PC.481_2', 'Control', '20070314'],
['PC.593_2', 'Control', '20071210'],
['PC.607_2', 'Fast', '20071112'],
['PC.634_2', 'Fast', '20080116'],
['PC.635_2', 'Fast', '20080116'],
['PC.636_2', 'Fast', '20080116']]
COORDS_DATA = array([
[-0.2, -0.1, 0.06, -0.06],
[-0.3, 0.04, -0.1, 0.15],
[0.1, -0.1, -0.2, 0.08],
[0.04, -0.01, 0.06, -0.34]])
BROKEN_MAPPING_FILE = [
['PC.354', 'Control', '3', '40', 'Control20061218'],
['PC.355', 'Control', 'y', '44', 'Control20061218'],
['PC.635', 'Fast', '9', 'x', 'Fast20080116'],
['PC.636', 'Fast', '12', '37.22', 'Fast20080116']]
BROKEN_MAPPING_FILE_2_VALUES = [
['PC.354', 'Control', '3', '40', 'Control20061218'],
['PC.355', 'Control', 'NA', '44', 'Control20061218'],
['PC.635', 'Fast', 'NA', 'x', 'Fast20080116'],
['PC.636', 'Fast', '12', '37.22', 'Fast20080116']]
UNSANITZIED_MAPPING_DATA = [
['PC.354', "Dr. Bronner's", 'Cont"rol', '20061218',
'Control_mouse_I.D._354'],
['PC.355', 'AACTCGTCGATG', "Con''trol", '20061218',
'Control_mouse_I.D._355'],
["PC'356", 'ACAGACCACTCA', 'Control', '20061126',
'Control_mouse_I.D._"356'],
['PC.481', 'AC"AGC"ACTAG', 'Control', '20070314',
'Control_mouse_I.D._481'],
['PC.593', 'AGCAGCACTTGT', 'Control', '20071210',
'Control_mouse_I.D._593']]
if __name__ == "__main__":
main()