def test_get_rarefaction_data(self):
"""get_rarefaction_data: This tests the functionality of taking a
rarefaction file and returns three values"""
obs1, obs2, obs3 = get_rarefaction_data(self.rarefaction_file_data, self.col_headers2)
exp1 = [[1.0, 3.0]]
exp2 = [10.0, 10.0]
exp3 = ["Sample1", "Sample2"]
self.assertEqual(obs1, exp1)
self.assertEqual(obs2, exp2)
self.assertEqual(obs3, exp3)
def test_get_rarefaction_data(self):
'''get_rarefaction_data: This tests the functionality of taking a
rarefaction file and returns three values'''
obs1,obs2,obs3 = get_rarefaction_data(self.rarefaction_file_data, \
self.col_headers2)
exp1 = [[1.0, 3.0]]
exp2 = [10.0, 10.0]
exp3 = ['Sample1', 'Sample2']
self.assertEqual(obs1, exp1)
self.assertEqual(obs2, exp2)
self.assertEqual(obs3, exp3)
def setUp(self):
"""define some top-level data"""
self.data = {}
self.data['xaxis'] = [10.0]
self.sample_dict = {'Sample1': {10.00: [1.3276140000000001]}}
self.data['yvals'] = {'Sample1': [1.3276140000000001]}
self.data['err'] = {'Sample1': [.1]}
self.xmax = 140
self.ymax = 20
self.std_type = 'stddev'
self.ops = ['Sample1']
self.mapping_category = 'SampleID'
self.imagetype = 'png'
self.resolution = 70
self.mapping_lookup = {'SampleID-Sample1': 'col_0_row_0'}
self.data['map'] = [['SampleID', 'Day'], ['Sample1', 'Day1']]
self.color_prefs={'SampleID': {'column': 'SampleID', 'color': \
{'Sample1': '#ff0000'}}}
self.groups = {'Sample1': ['Sample1']}
self.background_color = 'black'
self.label_color = 'white'
self.labelname = 'SampleID'
self.rare_data={'color': {'Sample1': '#ff0000'}, \
'series': {'Sample1': [2.0515300000000001],}, \
'headers': ['test.txt','SampleID'], 'xaxis': [10.0], \
'error': {'Sample1': [0.0]}, 'options': ['Sample1']}
self.fpath = '/tmp/'
self.output_dir = '/tmp/'
self.metric_name = 'test'
self._paths_to_clean_up = []
self._folders_to_cleanup = []
self.rarefaction_file_data = [[10.0, 0.0, 1.0], [10.0, 1.0, 3.0]]
d = {'redtowhite3_0': '#7fff00', 'redtowhite3_1': '#7fff00'}
self.data_colors = color_dict_to_objects(d)
self.colors = {'Sample1': 'redtowhite3_0', 'Sample2': 'redtowhite3_1'}
self.colors2 = {'Sample1': 'redtowhite3_0'}
self.mappingfile = [
'#SampleID\tSex\tAge', '123\tF\t32', '234\tM\t30', '345\tM\t32'
]
#self.p_mappingfile = parse_mapping_file(self.mappingfile,\
# strip_quotes=True)
self.rarefactionfile=[\
'\tsequences per sample\titeration\t123\t234\t345',
'rare10.txt\t10\t0\t1.99181\t0.42877\t2.13996',
'rare10.txt\t10\t1\t2.07163\t0.42877\t2.37055',
'rare310.txt\t310\t0\t8.83115\t0.42877\t11.00725',
'rare310.txt\t310\t1\t10.05242\t0.42877\t8.24474',
'rare610.txt\t610\t0\t12.03067\t0.42877\t11.58928',
'rare610.txt\t610\t1\t12.9862\t0.42877\t11.58642']
self.rares = {'test.txt': (['', 'sequences per sample', 'iteration', \
'Sample1'], [], ['rare1.txt', 'rare2.txt'], \
[[10.0, 2.0, 7.0, 7.0, 9.0], [10.0, 2.0, 7.0, 7.0, 9.0]])}
self.col_headers, self.comments, self.rarefaction_fns, \
self.rarefaction_data = parse_rarefaction(self.rarefactionfile)
self.matrix, self.seqs_per_samp, self.sampleIDs = \
get_rarefaction_data(self.rarefaction_data, self.col_headers)
self.ave_seqs_per_sample1 = {'Sample1':[2.03172,9.4417849999999994,\
12.508435]}
self.ave_seqs_per_sample = {'123':[2.03172,9.4417849999999994,\
12.508435],'234':[0.42876999999999998,0.42876999999999998,\
0.42876999999999998],'345':[2.255255,9.625995,11.58785]}
self.collapsed_ser_sex = {'M':[1.3420125000000001,5.0273824999999999,\
6.0083099999999998], 'F':[2.03172,9.4417849999999994,12.508435]}
self.err_ser_sex = {'M':[0.91324250000000007,4.5986124999999998,\
5.5795399999999997],'F':[0.0,0.0,0.0]}
self.rarefaction_legend_mat_init = {'test': {'SampleID': {}}}
self.col_headers2=['', 'sequences per sample', 'iteration', 'Sample1', \
'Sample2']
self.rarefaction_data_mat = {
'SampleID': {
'Sample1': {
'test': {
'ave': [' 7.000'],
'err': [' nan']
}
}
}
}
self.rarefaction_legend_mat = {
'test': {
'samples': {
'Sample1': {
'color': '#ff0000',
'link': 'html_plots/testcol_0_row_0.png'
}
},
'groups': {
'SampleID': {
'Sample1': {
'groupcolor': '#ff0000',
'groupsamples': ['Sample1']
}
}
}
}
}
self.exp_err_series_ave = {
'M': [1.571915, 6.49885, 8.1750183333333339]
}
def setUp(self):
"""define some top-level data"""
self.data={}
self.data['xaxis']=[10.0]
self.sample_dict={'Sample1':{10.00: [1.3276140000000001]}}
self.data['yvals']={'Sample1': [1.3276140000000001]}
self.data['err']={'Sample1': [.1]}
self.xmax=140
self.ymax=20
self.std_type='stddev'
self.ops=['Sample1']
self.mapping_category='SampleID'
self.imagetype='png'
self.resolution=70
self.mapping_lookup={'SampleID-Sample1':'col_0_row_0'}
self.data['map']=[['SampleID','Day'],['Sample1','Day1']]
self.color_prefs={'SampleID': {'column': 'SampleID', 'color': \
{'Sample1': '#ff0000'}}}
self.groups={'Sample1':['Sample1']}
self.background_color='black'
self.label_color='white'
self.labelname='SampleID'
self.rare_data={'color': {'Sample1': '#ff0000'}, \
'series': {'Sample1': [2.0515300000000001],}, \
'headers': ['test.txt','SampleID'], 'xaxis': [10.0], \
'error': {'Sample1': [0.0]}, 'options': ['Sample1']}
self.fpath='/tmp/'
self.output_dir='/tmp/'
self.metric_name='test'
self._paths_to_clean_up = []
self._folders_to_cleanup = []
self.rarefaction_file_data=[[10.0, 0.0, 1.0], [10.0, 1.0, 3.0]]
d = {'redtowhite3_0':'#7fff00','redtowhite3_1':'#7fff00'}
self.data_colors = color_dict_to_objects(d)
self.colors={'Sample1':'redtowhite3_0','Sample2':'redtowhite3_1'}
self.colors2={'Sample1':'redtowhite3_0'}
self.mappingfile = ['#SampleID\tSex\tAge',
'123\tF\t32',
'234\tM\t30',
'345\tM\t32']
#self.p_mappingfile = parse_mapping_file(self.mappingfile,\
# strip_quotes=True)
self.rarefactionfile=[\
'\tsequences per sample\titeration\t123\t234\t345',
'rare10.txt\t10\t0\t1.99181\t0.42877\t2.13996',
'rare10.txt\t10\t1\t2.07163\t0.42877\t2.37055',
'rare310.txt\t310\t0\t8.83115\t0.42877\t11.00725',
'rare310.txt\t310\t1\t10.05242\t0.42877\t8.24474',
'rare610.txt\t610\t0\t12.03067\t0.42877\t11.58928',
'rare610.txt\t610\t1\t12.9862\t0.42877\t11.58642']
self.rares = {'test.txt': (['', 'sequences per sample', 'iteration', \
'Sample1'], [], ['rare1.txt', 'rare2.txt'], \
[[10.0, 2.0, 7.0, 7.0, 9.0], [10.0, 2.0, 7.0, 7.0, 9.0]])}
self.col_headers, self.comments, self.rarefaction_fns, \
self.rarefaction_data = parse_rarefaction(self.rarefactionfile)
self.matrix, self.seqs_per_samp, self.sampleIDs = \
get_rarefaction_data(self.rarefaction_data, self.col_headers)
self.ave_seqs_per_sample1 = {'Sample1':[2.03172,9.4417849999999994,\
12.508435]}
self.ave_seqs_per_sample = {'123':[2.03172,9.4417849999999994,\
12.508435],'234':[0.42876999999999998,0.42876999999999998,\
0.42876999999999998],'345':[2.255255,9.625995,11.58785]}
self.collapsed_ser_sex = {'M':[1.3420125000000001,5.0273824999999999,\
6.0083099999999998], 'F':[2.03172,9.4417849999999994,12.508435]}
self.err_ser_sex = {'M':[0.91324250000000007,4.5986124999999998,\
5.5795399999999997],'F':[0.0,0.0,0.0]}
self.rarefaction_legend_mat_init={'test': {'SampleID': {}}}
self.col_headers2=['', 'sequences per sample', 'iteration', 'Sample1', \
'Sample2']
self.rarefaction_data_mat={'SampleID': {'Sample1': {'test': {'ave': [' 7.000'], 'err': [' nan']}}}}
self.rarefaction_legend_mat={'test': {'samples': {'Sample1': {'color': '#ff0000', 'link': 'html_plots/testcol_0_row_0.png'}}, 'groups': {'SampleID': {'Sample1': {'groupcolor': '#ff0000', 'groupsamples': ['Sample1']}}}}}
self.exp_err_series_ave={'M': [1.571915, 6.49885, 8.1750183333333339]}
def setUp(self):
"""define some top-level data"""
self.data = {}
self.data["xaxis"] = [10.0]
self.sample_dict = {"Sample1": {10.00: [1.3276140000000001]}}
self.data["yvals"] = {"Sample1": [1.3276140000000001]}
self.data["err"] = {"Sample1": [0.1]}
self.xmax = 140
self.ymax = 20
self.std_type = "stddev"
self.ops = ["Sample1"]
self.mapping_category = "SampleID"
self.imagetype = "png"
self.resolution = 70
self.mapping_lookup = {"SampleID-Sample1": "col_0_row_0"}
self.data["map"] = [["SampleID", "Day"], ["Sample1", "Day1"]]
self.color_prefs = {"SampleID": {"column": "SampleID", "color": {"Sample1": "#ff0000"}}}
self.groups = {"Sample1": ["Sample1"]}
self.background_color = "black"
self.label_color = "white"
self.labelname = "SampleID"
self.rare_data = {
"color": {"Sample1": "#ff0000"},
"series": {"Sample1": [2.0515300000000001]},
"headers": ["test.txt", "SampleID"],
"xaxis": [10.0],
"error": {"Sample1": [0.0]},
"options": ["Sample1"],
}
self.fpath = "/tmp/"
self.output_dir = "/tmp/"
self.metric_name = "test"
self._paths_to_clean_up = []
self._folders_to_cleanup = []
self.rarefaction_file_data = [[10.0, 0.0, 1.0], [10.0, 1.0, 3.0]]
d = {"redtowhite3_0": "#7fff00", "redtowhite3_1": "#7fff00"}
self.data_colors = color_dict_to_objects(d)
self.colors = {"Sample1": "redtowhite3_0", "Sample2": "redtowhite3_1"}
self.colors2 = {"Sample1": "redtowhite3_0"}
self.mappingfile = ["#SampleID\tSex\tAge", "123\tF\t32", "234\tM\t30", "345\tM\t32"]
# self.p_mappingfile = parse_mapping_file(self.mappingfile,\
# strip_quotes=True)
self.rarefactionfile = [
"\tsequences per sample\titeration\t123\t234\t345",
"rare10.txt\t10\t0\t1.99181\t0.42877\t2.13996",
"rare10.txt\t10\t1\t2.07163\t0.42877\t2.37055",
"rare310.txt\t310\t0\t8.83115\t0.42877\t11.00725",
"rare310.txt\t310\t1\t10.05242\t0.42877\t8.24474",
"rare610.txt\t610\t0\t12.03067\t0.42877\t11.58928",
"rare610.txt\t610\t1\t12.9862\t0.42877\t11.58642",
]
self.rares = {
"test.txt": (
["", "sequences per sample", "iteration", "Sample1"],
[],
["rare1.txt", "rare2.txt"],
[[10.0, 2.0, 7.0, 7.0, 9.0], [10.0, 2.0, 7.0, 7.0, 9.0]],
)
}
self.col_headers, self.comments, self.rarefaction_fns, self.rarefaction_data = parse_rarefaction(
self.rarefactionfile
)
self.matrix, self.seqs_per_samp, self.sampleIDs = get_rarefaction_data(self.rarefaction_data, self.col_headers)
self.ave_seqs_per_sample1 = {"Sample1": [2.03172, 9.4417849999999994, 12.508435]}
self.ave_seqs_per_sample = {
"123": [2.03172, 9.4417849999999994, 12.508435],
"234": [0.42876999999999998, 0.42876999999999998, 0.42876999999999998],
"345": [2.255255, 9.625995, 11.58785],
}
self.collapsed_ser_sex = {
"M": [1.3420125000000001, 5.0273824999999999, 6.0083099999999998],
"F": [2.03172, 9.4417849999999994, 12.508435],
}
self.err_ser_sex = {"M": [0.91324250000000007, 4.5986124999999998, 5.5795399999999997], "F": [0.0, 0.0, 0.0]}
self.rarefaction_legend_mat_init = {"test": {"SampleID": {}}}
self.col_headers2 = ["", "sequences per sample", "iteration", "Sample1", "Sample2"]
self.rarefaction_data_mat = {"SampleID": {"Sample1": {"test": {"ave": [" 7.000"], "err": [" nan"]}}}}
self.rarefaction_legend_mat = {
"test": {
"samples": {"Sample1": {"color": "#ff0000", "link": "html_plots/testcol_0_row_0.png"}},
"groups": {"SampleID": {"Sample1": {"groupcolor": "#ff0000", "groupsamples": ["Sample1"]}}},
}
}
self.exp_err_series_ave = {"M": [1.571915, 6.49885, 8.1750183333333339]}