from __future__ import print_function # so that print behaves like python 3.x not a special lambda statement import sys sys.path.append('../../') import logomaker import numpy as np import pandas as pd import matplotlib.pyplot as plt global_success_counter = 0 global_fail_counter = 0 # Common success and fail lists bool_fail_list = [0, -1, 'True', 'x', 1] bool_success_list = [False, True] # helper method for functional test_for_mistake def test_for_mistake(func, *args, **kw): """ Run a function with the specified parameters and register whether success or failure was a mistake parameters ---------- func: (function or class constructor) An executable function to which *args and **kwargs are passed. return ------ None. """ global global_fail_counter global global_success_counter # print test number test_num = global_fail_counter + global_success_counter print('Test # %d: ' % test_num, end='') #print('Test # %d: ' % test_num) # Run function obj = func(*args, **kw) # Increment appropriate counter if obj.mistake: global_fail_counter += 1 else: global_success_counter += 1 def test_parameter_values(func, var_name=None, fail_list=[], success_list=[], **kwargs): """ Tests predictable success & failure of different values for a specified parameter when passed to a specified function parameters ---------- func: (function) Executable to test. Can be function or class constructor. var_name: (str) Name of variable to test. If not specified, function is tested for success in the absence of any passed parameters. fail_list: (list) List of values for specified variable that should fail success_list: (list) List of values for specified variable that should succeed **kwargs: Other keyword variables to pass onto func. return ------ None. """ # If variable name is specified, test each value in fail_list # and success_list if var_name is not None: # User feedback print("Testing %s() parameter %s ..." % (func.__name__, var_name)) # Test parameter values that should fail for x in fail_list: kwargs[var_name] = x test_for_mistake(func=func, should_fail=True, **kwargs) # Test parameter values that should succeed for x in success_list: kwargs[var_name] = x test_for_mistake(func=func, should_fail=False, **kwargs) print("Tests passed: %d. Tests failed: %d.\n" % (global_success_counter, global_fail_counter)) # Otherwise, make sure function without parameters succeeds else: # User feedback print("Testing %s() without parameters." % func.__name__) # Test function test_for_mistake(func=func, should_fail=False, **kwargs) # close all figures that might have been generated plt.close('all') def test_Logo(): # df inputs that successfully execute when entered into Logo. good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) good_prob_df = logomaker.get_example_matrix('ss_probability_matrix', print_description=False) random_df = pd.DataFrame(np.random.randint(0, 3, size=(10, 4)), columns=list('ACGT')) # df inputs that fail when entered into Logo. bad_df1 = 'x' # test parameter df test_parameter_values(func=logomaker.Logo, var_name='df',fail_list=[bool_fail_list,bad_df1], success_list=[good_crp_df,random_df]) # test parameter colors test_parameter_values(func=logomaker.Logo, var_name='color_scheme', fail_list=['x','bad_color_name',3], success_list=['classic', 'grays', 'charge','salmon'], df=good_crp_df) # test parameter font names test_parameter_values(func=logomaker.Logo, var_name='font_name', fail_list=[True, None, good_crp_df], success_list=['DejaVu Sans', 'Arial Rounded MT Bold', 'Times New Roman'], df=good_crp_df) # test parameter stack_order test_parameter_values(func=logomaker.Logo, var_name='stack_order', fail_list=['incorrect argument', 0.0, None], success_list=['small_on_top', 'big_on_top', 'fixed'], df=good_crp_df) # test parameter center_values test_parameter_values(func=logomaker.Logo, var_name='center_values', fail_list=['incorrect argument', 0.0, None], success_list=[True, False], df=good_crp_df) # test parameter baseline_width test_parameter_values(func=logomaker.Logo, var_name='baseline_width', fail_list=['incorrect argument', -0.1, None], success_list=[0,0.5,3], df=good_crp_df) # test parameter flip_below test_parameter_values(func=logomaker.Logo, var_name='flip_below', fail_list=['incorrect argument', -0.1, None], success_list=[True, False], df=good_crp_df) # test parameter shade_below test_parameter_values(func=logomaker.Logo, var_name='shade_below', fail_list=['incorrect argument', -0.1, 1.4, None], success_list=[0, 0.0, 0.5, 1, 1.0], df=good_crp_df) # test parameter fade_below test_parameter_values(func=logomaker.Logo, var_name='fade_below', fail_list=['incorrect argument', -0.1, 1.4, None], success_list=[0, 0.0, 0.5, 1, 1.0], df=good_crp_df) # test parameter fade_probabilities test_parameter_values(func=logomaker.Logo, var_name='fade_probabilities', fail_list=['incorrect argument', -0.1, 1.4, None], success_list=[True, False], df=good_prob_df) # test parameter vsep test_parameter_values(func=logomaker.Logo, var_name='vsep', fail_list=['incorrect argument', -0.1, None], success_list=[0.0, 0,0.3,10], df=good_crp_df) # test parameter vsep # TODO: note that a value of True/False is still causing a logo to be drawn, eventhough draw_now = False test_parameter_values(func=logomaker.Logo, var_name='show_spines', fail_list=['incorrect argument', -0.1], success_list=[None, True, False], df=good_crp_df) # test parameter zorder. Need to review zorder's input check in Logo test_parameter_values(func=logomaker.Logo, var_name='zorder', fail_list=['incorrect argument'], success_list=[0, 1, 3], df=good_crp_df) # test parameter figsize test_parameter_values(func=logomaker.Logo, var_name='figsize', fail_list=['incorrect argument', -0.1, [-1,-1],[-1],[0,0],['x','y'],(1,2,3)], success_list=[(10, 2.5),[5,5]], df=good_crp_df) # validate ax _, temp_ax = plt.subplots(figsize=[3, 3]) test_parameter_values(func=logomaker.Logo, var_name='ax', fail_list=['x',1,True], success_list=[temp_ax, None], df=good_crp_df) def test_Logo_style_glyphs(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # test parameter color_scheme test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs,var_name='color_scheme', fail_list=['bad_color_scheme',1,True], success_list=['classic','gray','salmon']) # TODO: how should we test kwargs for this (and other) methods? def test_Logo_fade_glyphs_in_probability_logo(): good_prob_df = logomaker.get_example_matrix('ss_probability_matrix', print_description=False) # test parameter v_alpha0 test_parameter_values(func=logomaker.Logo(good_prob_df).fade_glyphs_in_probability_logo, var_name='v_alpha0', fail_list=[-1,1.1,1,1.0,'xxx',True], success_list=[0,0.0,0.999,0.5]) # TODO: a value of True v_alpha_1 works now, this should probably be fixed. # test parameter v_alpha1 test_parameter_values(func=logomaker.Logo(good_prob_df).fade_glyphs_in_probability_logo, var_name='v_alpha1', fail_list=[1.1, -1, 'xxx'], success_list=[0.999, 0.5,1.0]) def test_Logo_style_glyphs_below(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # test parameter color test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below, var_name='color', fail_list=[0,'xxx',True,[0,0,-1]], success_list=['red', [1,1,1], [0,0,0],[0.1,0.2,0.3], None]) # test parameter alpha test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below, var_name='alpha', fail_list=[-1,'x',1.1], success_list=[0,1,0.5]) # test parameter shade test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below, var_name='shade', fail_list=[-1,'x',1.1], success_list=[0,1,0.5]) # test parameter fade test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below, var_name='fade', fail_list=[-1,'x',1.1], success_list=[0,1,0.5]) # test parameter flip test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_below, var_name='flip', fail_list=bool_fail_list, success_list=bool_success_list) def test_Logo_style_single_glyph(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # test parameter p test_parameter_values(func=logomaker.Logo(good_crp_df).style_single_glyph, var_name='p', fail_list=[-1,'x',1.1,10000], success_list=[0,1,10],c='A') # test parameter c test_parameter_values(func=logomaker.Logo(good_crp_df).style_single_glyph, var_name='c', fail_list=[-1, 'x', 1.1], success_list=['A','C','G','T'], p=1) def test_Logo_style_glyphs_in_sequence(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # randomly make up a sequence of the correct length test_good_sequence = np.random.choice(['A', 'C', 'G', 'T'], size=26, p=[0.25, 0.25, 0.25, 0.25]) test_good_sequence = "".join(test_good_sequence) # randomly make up a sequence of the incorrect length test_bad_sequence = np.random.choice(['A', 'C', 'G', 'T'], size=10, p=[0.25, 0.25, 0.25, 0.25]) test_bad_sequence = "".join(test_bad_sequence) # test parameter sequence test_parameter_values(func=logomaker.Logo(good_crp_df).style_glyphs_in_sequence, var_name='sequence', fail_list=[-1, 'x', 1.1, test_bad_sequence], success_list=[test_good_sequence]) def test_Logo_highlight_position(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # test parameter p test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position, var_name='p', fail_list=['x',1.5], success_list=[0, 1, 10]) def test_Logo_highlight_position_range(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # test parameter pmin test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position_range, var_name='pmin', fail_list=['x', 20], success_list=[0, 1, 10], pmax=15) # test parameter pmax test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position_range, var_name='pmax', fail_list=['x', 1], success_list=[5.5, 6, 10], pmin=5) # test parameter padding test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position_range, var_name='padding', fail_list=['x', -1], success_list=[-0.5, 0, 10], pmin=5,pmax=10) # test parameter color test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position_range, var_name='color', fail_list=['x', 1,True,'wrong_color'], success_list=['pink','red',[1,1,1]], pmin=5, pmax=10) # test parameter edgecolor test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position_range, var_name='edgecolor', fail_list=['x', 1, True, 'wrong_color'], success_list=[None,'pink', 'red', [1, 1, 1]], pmin=5, pmax=10) # test parameter floor test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position_range, var_name='floor', fail_list=['x', 10], success_list=[-1,1,None], pmin=5, pmax=10) # test parameter ceiling test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position_range, var_name='ceiling', fail_list=['x', -10], success_list=[-1, 1, None], pmin=5, pmax=10) # test parameter zorder. Note that a value of False passes for this parameter. This should be fixed. test_parameter_values(func=logomaker.Logo(good_crp_df).highlight_position_range, var_name='zorder', fail_list=['x', None], success_list=[-1, 0.5, 1], pmin=5, pmax=10) def test_Logo_draw_baseline(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # test parameter zorder test_parameter_values(func=logomaker.Logo(good_crp_df).draw_baseline, var_name='zorder', fail_list=['x', None], success_list=[-1, 0.5, 1]) # test parameter color test_parameter_values(func=logomaker.Logo(good_crp_df).draw_baseline, var_name='color', fail_list=['x', 1, True, 'wrong_color'], success_list=['pink', 'red', [1, 1, 1]]) # test parameter linewidth test_parameter_values(func=logomaker.Logo(good_crp_df).draw_baseline, var_name='linewidth', fail_list=['x', -1, '1', None], success_list=[0,1,1.5,2]) def test_Logo_style_xticks(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # test parameter anchor test_parameter_values(func=logomaker.Logo(good_crp_df).style_xticks, var_name='anchor', fail_list=['x', None, 0.5, 1.0], success_list=[-1, 1, 2]) # test parameter spacing test_parameter_values(func=logomaker.Logo(good_crp_df).style_xticks, var_name='spacing', fail_list=['x', None, 0, 0.5], success_list=[1, 2]) # test parameter fmt # TODO: fmt = 'x' seems to passing in the following. This should be fixed. test_parameter_values(func=logomaker.Logo(good_crp_df).style_xticks, var_name='fmt', fail_list=[None, 0], success_list=['%d']) # test parameter rotation test_parameter_values(func=logomaker.Logo(good_crp_df).style_xticks, var_name='rotation', fail_list=[None, 'x'], success_list=[-12,0,1.4,200]) def test_Logo_style_spines(): good_crp_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) # test parameter anchor test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines, var_name='spines', fail_list=['x', None, 0.5, 1.0,'top'], success_list=[('top', 'bottom', 'left', 'right'), ['top', 'bottom', 'left', 'right'], ('top', 'bottom', 'left'), ('top', 'bottom'), ['top']]) # test parameter visible test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines, var_name='visible', fail_list=bool_fail_list, success_list=bool_success_list) # test parameter color test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines, var_name='color', fail_list=['wrong_color',3,[0.5,0.5,0.5,0.5]], success_list=['black','green',[0.4,0.5,1.0]]) # test parameter linewidth test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines, var_name='linewidth', fail_list=['xxx',-1], success_list=[0.0,0,1]) # test parameter bounds test_parameter_values(func=logomaker.Logo(good_crp_df).style_spines, var_name='bounds', fail_list=['xxx', -1], success_list=[None,[0,1]]) def test_transform_matrix(): good_crp_weight_df = logomaker.get_example_matrix('crp_energy_matrix', print_description=False) good_crp_counts_df = logomaker.get_example_matrix('crp_counts_matrix', print_description=False) # test parameter df test_parameter_values(func=logomaker.transform_matrix, var_name='df', fail_list=['x',good_crp_weight_df,None], success_list=[good_crp_counts_df], from_type='counts', to_type='probability') test_parameter_values(func=logomaker.transform_matrix, var_name='df', fail_list=[], success_list=[good_crp_counts_df], from_type='counts', to_type='weight') test_parameter_values(func=logomaker.transform_matrix, var_name='df', fail_list=[], success_list=[good_crp_counts_df], from_type='counts', to_type='information') # test parameter center_values test_parameter_values(func=logomaker.transform_matrix, var_name='center_values', fail_list=bool_fail_list, success_list=bool_success_list, df= good_crp_counts_df) # test parameter normalize_values test_parameter_values(func=logomaker.transform_matrix, var_name='normalize_values', fail_list=bool_fail_list, success_list=bool_success_list, df=good_crp_counts_df) # test parameter from_type test_parameter_values(func=logomaker.transform_matrix, var_name='from_type', fail_list=[1,'x',None], success_list=['counts'], df=good_crp_counts_df,to_type='probability') # test parameter to_type test_parameter_values(func=logomaker.transform_matrix, var_name='to_type', fail_list=[1, 'x', None], success_list=['probability','weight','information'], df=good_crp_counts_df, from_type='counts') # test parameter background test_parameter_values(func=logomaker.transform_matrix, var_name='background', fail_list=[1, 'x', [-1,1,1,1]], success_list=[None, [0.25,0.25,0.25,0.25]], df=good_crp_counts_df, from_type='counts', to_type='information') # test parameter pseudocount test_parameter_values(func=logomaker.transform_matrix, var_name='pseudocount', fail_list=[None, 'x', -1], success_list=[0,1,10], df=good_crp_counts_df, from_type='counts', to_type='probability') def test_sequence_to_matrix(): # test parameter seq test_parameter_values(func=logomaker.sequence_to_matrix, var_name='seq', fail_list=[None, 3, True], success_list=['ACGT', '!@#$', 'logomaker']) # test parameter cols test_parameter_values(func=logomaker.sequence_to_matrix, var_name='cols', fail_list=[0, True], success_list=[None, ['A','C','G','T']],seq='ACGTACGT') # test parameter alphabet test_parameter_values(func=logomaker.sequence_to_matrix, var_name='alphabet', fail_list=[0, True, 'xxx'], success_list=[None,'dna'], seq='ACGTACGT') test_parameter_values(func=logomaker.sequence_to_matrix, var_name='alphabet', fail_list=[], success_list=['rna'], seq='ACGUACGU') test_parameter_values(func=logomaker.sequence_to_matrix, var_name='alphabet', fail_list=[], success_list=['protein'], seq='LMWA') # test parameter is_iupac test_parameter_values(func=logomaker.sequence_to_matrix, var_name='is_iupac', fail_list=bool_fail_list, success_list=bool_success_list, seq='ACGTACGT') # test parameter to_type test_parameter_values(func=logomaker.sequence_to_matrix, var_name='to_type', fail_list=[0, True, 'xxx'], success_list=['probability','weight','information'], seq='ACGTACGT') # test parameter center_weights test_parameter_values(func=logomaker.sequence_to_matrix, var_name='center_weights', fail_list=bool_fail_list, success_list=bool_success_list, seq='ACGTACGT',to_type='weight') def test_alignment_to_matrix(): # get sequences from file with logomaker.open_example_datafile('crp_sites.fa', print_description=False) as f: raw_seqs = f.readlines() seqs = [seq.strip() for seq in raw_seqs if ('#' not in seq) and ('>') not in seq] # test parameter sequences test_parameter_values(func=logomaker.alignment_to_matrix,var_name='sequences', fail_list = [0,'x',['AACCT','AACGATA']], success_list = [seqs,['ACA','GGA']]) # test parameter counts # TODO: need to find a working example for counts other than None test_parameter_values(func=logomaker.alignment_to_matrix, var_name='counts', fail_list=[0, 'x', -1], success_list=[None],sequences=['ACA', 'GGA']) # test parameter to_type test_parameter_values(func=logomaker.alignment_to_matrix, var_name='to_type', fail_list=[0, True, 'xxx'], success_list=['counts','probability', 'weight', 'information'], sequences=seqs) # test parameter background test_parameter_values(func=logomaker.alignment_to_matrix, var_name='background', fail_list=[1, 'x'], success_list=[None, [0.25,0.25,0.25,0.25]], sequences=seqs) # test parameter characters_to_ignore test_parameter_values(func=logomaker.alignment_to_matrix, var_name='characters_to_ignore', fail_list=[1, 0.5,True,None], success_list=['A','C','G'], sequences=seqs) # test parameter center_weights test_parameter_values(func=logomaker.alignment_to_matrix, var_name='center_weights', fail_list=bool_fail_list, success_list=bool_success_list, sequences=seqs) # test parameter pseudocount test_parameter_values(func=logomaker.alignment_to_matrix, var_name='pseudocount', fail_list=[None, 'x', -1], success_list=[0, 1, 10], sequences=seqs) def test_saliency_to_matrix(): # load saliency data with logomaker.open_example_datafile('nn_saliency_values.txt', print_description=False) as f: saliency_data_df = pd.read_csv(f, comment='#', sep='\t') # test parameter seq test_parameter_values(func=logomaker.saliency_to_matrix, var_name='seq', fail_list=[None, 'x', -1], success_list=[saliency_data_df['character']], values=saliency_data_df['value']) # test parameter values test_parameter_values(func=logomaker.saliency_to_matrix, var_name='values', fail_list=[None, 'x', -1], success_list=[saliency_data_df['value']], seq=saliency_data_df['character']) # test parameter cols test_parameter_values(func=logomaker.saliency_to_matrix, var_name='cols', fail_list=[-1,'x'], success_list=[None,['A','C','G','T']], seq=saliency_data_df['character'],values=saliency_data_df['value']) # test parameter alphabet test_parameter_values(func=logomaker.saliency_to_matrix, var_name='alphabet', fail_list=[0, True, 'xxx'], success_list=[None,'dna'], seq=saliency_data_df['character'], values=saliency_data_df['value']) def test_Glyph(): fig, ax = plt.subplots(figsize=[7, 3]) # set bounding box ax.set_xlim([0, 2]) ax.set_ylim([0, 1]) # test parameter p # TODO: need to fix fail_list bugs for parameter p test_parameter_values(func=logomaker.Glyph,var_name='p', fail_list=[],success_list=[0,1,10, 0.5], c='A', ax=ax, floor=0, ceiling=1) # test parameter c test_parameter_values(func=logomaker.Glyph, var_name='c', fail_list=[0,0.1,None], success_list=['A','C','x'], p=1, ax=ax, floor=0, ceiling=1) # test parameter floor test_parameter_values(func=logomaker.Glyph, var_name='floor', fail_list=['x',2, None], success_list=[0,0.1,0.5], p=1, ax=ax, ceiling=1, c='A') # test parameter ceiling test_parameter_values(func=logomaker.Glyph, var_name='ceiling', fail_list=['x', -1, None], success_list=[0, 0.1, 0.5], p=1, ax=ax, floor=0, c='A') # test parameter ax test_parameter_values(func=logomaker.Glyph, var_name='ax', fail_list=['x', -1], success_list=[None,ax], p=1, ceiling=1, floor=0, c='A') # test parameter width test_parameter_values(func=logomaker.Glyph, var_name='width', fail_list=['x', -1], success_list=[0.1,1,10], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter vpad test_parameter_values(func=logomaker.Glyph, var_name='vpad', fail_list=['x', -1, None, 1], success_list=[0, 0.9, 0.5], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter font_name test_parameter_values(func=logomaker.Glyph, var_name='font_name', fail_list=[-1], success_list=['DejaVu Sans'], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter font_weight test_parameter_values(func=logomaker.Glyph, var_name='font_weight', fail_list=[-1,'xxx'], success_list=['bold',5, 'normal'], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter color test_parameter_values(func=logomaker.Glyph, var_name='color', fail_list=[-1, 'xxx'], success_list=['red', [1,1,1], [0,0,0],[0.1,0.2,0.3]], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter edgecolor test_parameter_values(func=logomaker.Glyph, var_name='edgecolor', fail_list=[-1, 'xxx'], success_list=['black', [1, 1, 1], [0, 0, 0], [0.1, 0.2, 0.3]], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter edgewidth test_parameter_values(func=logomaker.Glyph, var_name='edgewidth', fail_list=['x', -1, None], success_list=[0, 0.9, 0.5], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter dont_stretch_more_than test_parameter_values(func=logomaker.Glyph, var_name='dont_stretch_more_than', fail_list=[-1, None], success_list=['E','A'], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter flip test_parameter_values(func=logomaker.Glyph, var_name='flip', fail_list=bool_fail_list, success_list=bool_success_list, p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter mirror test_parameter_values(func=logomaker.Glyph, var_name='mirror', fail_list=bool_fail_list, success_list=bool_success_list, p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter zorder test_parameter_values(func=logomaker.Glyph, var_name='zorder', fail_list=['x'], success_list=[0,0.5,1,5], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter alpha test_parameter_values(func=logomaker.Glyph, var_name='alpha', fail_list=[1.1, -1, 'xxx'], success_list=[0.999, 0.5, 1.0], p=1, ceiling=1, floor=0, c='A', ax=ax) # test parameter figsize test_parameter_values(func=logomaker.Glyph, var_name='figsize', fail_list=['incorrect argument', ['x', 'y'], (1, 2, 3),[1,-1]], success_list=[(10, 2.5), [5, 5]], p=1, ceiling=1, floor=0, c='A', ax=ax) def test_logomaker_get_data_methods(): # testing parameter name in get_example_matrix test_parameter_values(func=logomaker.get_example_matrix, var_name='name', fail_list = ['wrong argument', -1], success_list=['crp_energy_matrix','ww_counts_matrix'], print_description=False) # testing parameter print_description in get_example_matrix test_parameter_values(func=logomaker.get_example_matrix, var_name='print_description', fail_list=bool_fail_list, success_list=bool_success_list, name='crp_energy_matrix') # testing parameter name in open_example_datafile test_parameter_values(func=logomaker.open_example_datafile, var_name='name', fail_list=['wrong argument', -1], success_list=['nn_saliency_values.txt', 'ss_sequences.txt'], print_description=False) # testing parameter print_description in open_example_datafile test_parameter_values(func=logomaker.open_example_datafile, var_name='print_description', fail_list=bool_fail_list, success_list=bool_success_list, name='nn_saliency_values.txt') def test_demo(): test_parameter_values(func=logomaker.demo,var_name='name', fail_list=[0, True, 'xxx'], success_list=['crp', 'fig1b']) plt.close('all') def run_tests(): """ Run all Logomaker functional tests. There are 547 tests as of 14 May 2019. parameters ---------- None. return ------ None. """ # run tests for the Logo class and it's helper methods test_Logo() test_Logo_style_glyphs() test_Logo_fade_glyphs_in_probability_logo() test_Logo_style_glyphs_below() test_Logo_style_single_glyph() test_Logo_style_glyphs_in_sequence() test_Logo_highlight_position() test_Logo_highlight_position_range() test_Logo_draw_baseline() test_Logo_style_xticks() test_Logo_style_spines() # run tests for the methods in the matrix module test_transform_matrix() test_sequence_to_matrix() test_alignment_to_matrix() test_saliency_to_matrix() # run tests for the Glyph class test_Glyph() #test_demo() test_logomaker_get_data_methods() if __name__ == '__main__': run_tests()