test_make_distance_histograms.py

#!/usr/bin/env python
# file test_make_distance_histograms.py

__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.3.0"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Release"

from cogent.util.unit_test import TestCase, main
import shutil
from os import mkdir, listdir, path
from qiime.parse import parse_mapping_file, parse_distmat, group_by_field,\
    group_by_fields
from numpy import array, arange
from qiime.make_distance_histograms import between_sample_distances, \
    within_category_distances_grouped, between_category_distances_grouped, \
    within_category_distances, within_and_between_fields, \
    all_category_distances, draw_all_histograms, get_histogram_scale, \
    draw_histogram, make_nav_html, make_main_html, get_valid_indices, \
    distances_by_groups, write_distance_files, group_distances, \
    monte_carlo_group_distances, permute_for_monte_carlo, \
    _make_histogram_filenames, _make_relative_paths, \
    _make_random_filename, matplotlib_rgb_color, \
    average_colors, average_all_colors, assign_unassigned_colors,\
    assign_mapped_colors, monte_carlo_group_distances_within_between,\
    get_random_dists
    
from qiime.colors import data_colors
from collections import defaultdict

class DistanceHistogramsTests(TestCase):
    """Tests for make_distance_histograms.py
    """
        
    def tearDown(self):
        """clean up after running all tests.
        """
        shutil.rmtree(self.working_dir)
        
    def setUp(self):
        """setup data function for DistanceHistogramsTests."""
        self.working_dir = '/tmp/distance_histogram_tests/'
        try:
            mkdir(self.working_dir)
        except OSError: #except already exisits
            pass
        
        self.histogram_dir = path.join(self.working_dir,'histograms')
        try:
            mkdir(self.histogram_dir)
        except OSError: #except already exisits remove it and make a new one
            pass
            
        #Create distance matrix file
        self.dmat_file = self.working_dir+'dmat.txt'
        dmat_out = open(self.dmat_file,'w')
        dmat_out.write(DISTANCE_MATRIX_STRING)
        dmat_out.close()

        self.distance_header, self.dmat = \
            parse_distmat(open(self.dmat_file,'U'))
        
        #Create mapping file
        self.map_file = self.working_dir+'map.txt'
        map_out = open(self.map_file,'w')
        map_out.write(MAPPING_STRING)
        map_out.close()
        
        mapping, header, comments = parse_mapping_file(open(self.map_file,'U'))
        header[0] = '#'+header[0]
        header = [header]
        header.extend(mapping)
        self.mapping=header
        
        #Create prefs file
        self.prefs_file = self.working_dir+'prefs.txt'
        prefs_out = open(self.prefs_file,'w')
        prefs_out.write(str(PREFS))
        prefs_out.close()
        
        #Build single field dict for 'Treatment' field.
        self.single_field_treatment = defaultdict(dict)
        self.treatment_groups = group_by_field(self.mapping, 'Treatment')
        self.single_field_treatment['Treatment'] = \
            distances_by_groups(self.distance_header,self.dmat,\
                self.treatment_groups)
        self.paired_field_treatment = {'Treatment_to_Treatment':[\
            [('Control','Control'),('Fast','Fast'),\
                             array([[0.729,  0.8  ,  0.721, 0.765],
                                    [0.776,  0.744,  0.749, 0.677],
                                    [0.734,  0.777,  0.733, 0.724],
                                    [0.696,  0.675,  0.654, 0.696],
                                    [0.731,  0.758,  0.738, 0.737]])],\
            [('Control','Control'),('Control','Control'),\
                                 array([0.625,  0.623,  0.61 ,  0.577, 0.615,
                                        0.642,  0.673, 0.682,  0.737, 0.704])],\
            [('Fast','Fast'),('Fast','Fast'),\
                             array([0.718,  0.666, 0.727, 0.6, 0.578, 0.623])]
        ]}
        
        self.distances_file = self.working_dir+'distances_out.txt'
        dist_out = open(self.distances_file,'w')
        dist_out.write(DISTANCES_OUT)
        dist_out.close()
    
    def test_matplotlib_rgb_color(self):
        """matplotlib_rgb_color should correctly convert RGB to decimal.
        """
        test_data = [(255,255,255),(0,0,0),(255,0,100),(100,253,18)]
        exp = [(1.0,1.0,1.0),(0.,0.,0.),(1.,0.,0.39215686274509803),\
            (0.39215686274509803,0.99215686274509807,0.070588235294117646)]
        for t, e in zip(test_data,exp):
            self.assertEqual(matplotlib_rgb_color(t),e)
        
    def test_average_colors(self):
        """average_colors should properly average two RGB colors.
        """
        to_average = [((255,255,255),(0,0,0)),((255,0,100),(100,253,18))]
        exp = [(127.5,127.5,127.5),(177.5,126.5,59.)]
        for t,e in zip(to_average,exp):
            self.assertEqual(average_colors(t[0],t[1]),e)
    
    def test_average_all_colors(self):
        """average_all_colors should properly average all colors.
        """
        to_average = ['Treatment###FIELDDATA###Control_to_Fast',
                      'DOB###FIELDDATA###20070314_to_20061126']
        exp = {'Treatment###FIELDDATA###Control_to_Fast': \
            (0.0039215686274509803, 0.47843137254901963, 0.52745098039215688), 
            'DOB###FIELDDATA###20070314_to_20061126': (0.5, 0.0, 0.5)}
        self.assertEqual(average_all_colors(to_average,FIELD_TO_COLOR_PREFS),\
            exp)
    
    def test_assign_unassigned_colors(self):
        """assign_unassigned_colors should correctly assign unassigned.
        """
        unassigned = ['first','second','third']
        exp = {'second': (0.6470588235294118, 0.27843137254901962, 0.0), 
               'third': (0.9882352941176471, 0.77647058823529413, 
                         0.53333333333333333), 
               'first': (0.94901960784313721, 0.45098039215686275, 
                         0.015686274509803921)}
        self.assertEqual(assign_unassigned_colors(unassigned),exp)
    
    def test_assign_mapped_colors(self):
        """assign_mapped_colors should correctly assign mapped colors.
        """
        assigned = ['Treatment_Within_Control_Distances','DOB_Within_20070314']
        exp = {'Treatment_Within_Control_Distances':(0.,0.,1.),\
            'DOB_Within_20070314':(1.,0.,0.)}
        self.assertEqual(assign_mapped_colors(assigned,FIELD_TO_COLOR_PREFS),\
            exp)
        
    def test_between_sample_distances(self):
        """between_sample_distances should return correct result.
        """
        exp = {'All_Between_Sample_Distances':\
            [0.625, 0.623, 0.61, 0.577, 0.729,  0.8, 0.721, 0.765, 0.615,\
             0.642, 0.673, 0.776, 0.744, 0.749, 0.677,0.682, 0.737, 0.734,\
             0.777, 0.733, 0.724, 0.704, 0.696, 0.675, 0.654, 0.696, 0.731,\
             0.758, 0.738, 0.737, 0.718, 0.666, 0.727, 0.6, 0.578,0.623]}
        self.assertEqual(between_sample_distances(self.dmat),exp)
    
    def test_within_category_distances_grouped(self):
        """within_category_distances_grouped should return correct result.
        """
        exp = {'Treatment_All_Within_Category_Distances':\
            [0.625, 0.623, 0.61 , 0.577, 0.615, 0.642, 0.673, 0.682, 0.737, \
             0.704 ,0.718,  0.666, 0.727, 0.6, 0.578, 0.623]}
        self.assertEqual(within_category_distances_grouped(\
            self.single_field_treatment),exp)

    
    def test_between_category_distances_grouped(self):
        """between_category_distances_grouped should return correct result.
        """
        exp = {'Treatment_All_Between_Category_Distances':\
            [0.729,  0.8  ,  0.721, 0.765, 0.776,  0.744,  0.749, 0.677,\
             0.734,  0.777,  0.733, 0.724, 0.696,  0.675,  0.654, 0.696,\
             0.731,  0.758,  0.738, 0.737]}
        self.assertEqual(between_category_distances_grouped(\
            self.single_field_treatment),exp)

    def test_within_category_distances(self):
        """within_category_distances should return correct result.
        """
        exp = {'Treatment_Within_Control_Distances':\
                [0.625,  0.623,  0.61 ,  0.577, 0.615,\
                 0.642,  0.673, 0.682,  0.737, 0.704],\
               'Treatment_Within_Fast_Distances':\
                [0.718,  0.666, 0.727, 0.6, 0.578, 0.623]}
        self.assertEqual(within_category_distances(\
            self.single_field_treatment),exp)
    
    def test_within_and_between_fields(self):
        """within_and_between_fields should return correct result.
        """
        exp = {'Within_All_Fields':\
            [0.625, 0.623, 0.61 , 0.577, 0.615, 0.642, 0.673, 0.682, 0.737, \
             0.704 ,0.718,  0.666, 0.727, 0.6, 0.578, 0.623],\
               }
        
        self.assertEqual(within_and_between_fields(\
            self.paired_field_treatment),exp)
            
    
    def test_all_category_distances(self):
        """all_category_distances should return correct result.
        """
        exp = {'Treatment###FIELDDATA###Control_to_Control':\
                                       [0.625, 0.623, 0.61, 0.577, 0.615,\
                                        0.642, 0.673, 0.682, 0.737, 0.704],\
               'Treatment###FIELDDATA###Control_to_Fast':\
                                           [0.729,  0.8  ,  0.721, 0.765,\
                                            0.776,  0.744,  0.749, 0.677,\
                                            0.734,  0.777,  0.733, 0.724,\
                                            0.696,  0.675,  0.654, 0.696,\
                                            0.731,  0.758,  0.738, 0.737],\
               'Treatment###FIELDDATA###Fast_to_Fast':[0.718,  0.666, 0.727,\
                                            0.6, 0.578,0.623]
                }
        self.assertEqual(all_category_distances(\
            self.single_field_treatment),exp)
    
    def test_draw_all_histograms(self):
        """draw_all_histograms should return correct result.
        """
        distances_dict, label_to_histogram_filename = \
            draw_all_histograms(single_field = self.single_field_treatment, \
                                paired_field = self.paired_field_treatment, \
                                dmat=self.dmat,\
                                histogram_dir = self.histogram_dir,\
                                field_to_color_prefs = FIELD_TO_COLOR_PREFS,\
                                background_color='white')
        
        #Iterate through each histogram file and assure it exisits.
        for k,v in label_to_histogram_filename.items():
            obs_file = open(v,'U').read()
            self.assertGreaterThan(len(obs_file),0)
            

    def test_get_histogram_scale(self):
        """get_histogram_scale should return correct result.
        """
        distances_dict = {'All_Category_Pairs':{'Treatment_Control_to_Control':\
                               [0.625, 0.623, 0.61, 0.577, 0.615,\
                                0.642, 0.673, 0.682, 0.737, 0.704],\
       'Treatment_Control_to_Fast':[0.729,  0.8  ,  0.721, 0.765,\
                                    0.776,  0.744,  0.749, 0.677,\
                                    0.734,  0.777,  0.733, 0.724,\
                                    0.696,  0.675,  0.654, 0.696,\
                                    0.731,  0.758,  0.738, 0.737],\
       'Treatment_Fast_to_Fast':[0.718,  0.666, 0.727, 0.6, 0.578,\
                                 0.623]
        }}
        bins = arange(0,1.01,0.05)
        xscale_exp = (0.55,0.85)
        yscale_exp = (0.0,0.5)
        xscale_obs, yscale_obs = get_histogram_scale(distances_dict,bins)
        self.assertFloatEqual(xscale_obs,xscale_exp)
        self.assertFloatEqual(yscale_obs,yscale_exp)

    def test_draw_histogram(self):
        """draw_histogram should return correct result.
        """
        hist_outfile = self.working_dir+'test_hist.png'
        distances = [0.625, 0.623, 0.61 , 0.577, 0.615, 0.642, 0.673, 0.682, \
            0.737, 0.704 ,0.718,  0.666, 0.727, 0.6, 0.578, 0.623]
        color = 'blue'
        draw_histogram(distances,color,10,hist_outfile)
        obs_file = open(hist_outfile,'U').read()
        self.assertGreaterThan(len(obs_file),0)

    def test_make_nav_html(self):
        """make_nav_html should return correct result.
        """
        distances_dict, label_to_histogram_filename = \
            draw_all_histograms(single_field = self.single_field_treatment, \
                                paired_field = self.paired_field_treatment, \
                                dmat=self.dmat,\
                                histogram_dir = self.histogram_dir,\
                                field_to_color_prefs = FIELD_TO_COLOR_PREFS,\
                                background_color = 'white')
        nav_html_obs = \
            make_nav_html(distances_dict, label_to_histogram_filename)
        self.assertEqual(nav_html_obs, NAV_HTML)
        
    def test_make_main_html(self):
        """make_main_html should return correct result.
        """
        distances_dict, label_to_histogram_filename = \
            draw_all_histograms(single_field = self.single_field_treatment, \
                                paired_field = self.paired_field_treatment, \
                                dmat=self.dmat,\
                                histogram_dir = self.histogram_dir,\
                                field_to_color_prefs = FIELD_TO_COLOR_PREFS,\
                                background_color = 'white')
                                
        make_main_html(distances_dict=distances_dict, \
                       label_to_histogram_filename=label_to_histogram_filename,\
                       root_outdir=self.working_dir, \
                       outfile_name='QIIME_Distance_Histograms.html')
        main_html_obs = \
            open(self.working_dir+\
                'QIIME_Distance_Histograms.html','U').readlines()
                
        self.assertEqual(len(''.join(main_html_obs)),len(MAIN_HTML))

    def test_get_valid_indices(self):
        """get_valid_indices should return correct result.
        """
        control_ids = ['PC.354', 'PC.355', 'PC.356', 'PC.481', 'PC.593']
        exp_control_indices = [0,1,2,3,4]
        
        fast_ids = ['PC.607', 'PC.634', 'PC.635', 'PC.636']
        exp_fast_indices = [5,6,7,8]
        
        obs_control = get_valid_indices(self.distance_header, control_ids)
        self.assertEqual(obs_control, exp_control_indices)
        
        obs_fast = get_valid_indices(self.distance_header, fast_ids)
        self.assertEqual(obs_fast, exp_fast_indices)

    def test_distances_by_groups(self):
        """distances_by_groups should return correct result.
        """
        exp = [\
            ['Control','Fast',array([[0.729,  0.8  ,  0.721, 0.765],
                                    [0.776,  0.744,  0.749, 0.677],
                                    [0.734,  0.777,  0.733, 0.724],
                                    [0.696,  0.675,  0.654, 0.696],
                                    [0.731,  0.758,  0.738, 0.737]])],\
            ['Control','Control', array([0.625,  0.623,  0.61 ,  0.577, 0.615,
                                        0.642,  0.673, 0.682,  0.737, 0.704])],\
            ['Fast','Fast', array([0.718,  0.666, 0.727, 0.6, 0.578, 0.623])]
        ]
        
        obs = distances_by_groups(self.distance_header,self.dmat,\
            self.treatment_groups)
        self.assertEqual(obs,exp)

    def test_write_distance_files(self):
        """write_distance_files should return correct result.
        """
        exp_path = self.working_dir+'distances/dist_Treatment.xls'
        write_distance_files(self.single_field_treatment,\
            dir_prefix=self.working_dir)
        self.assertEqual(open(exp_path,'U').read(),
            open(self.distances_file,'U').read())

    def test_group_distances(self):
        """group_distances should return correct result.
        """
        single_field_exp = {'Treatment':[\
            ['Control','Fast',array([[0.729,  0.8  ,  0.721, 0.765],
                                    [0.776,  0.744,  0.749, 0.677],
                                    [0.734,  0.777,  0.733, 0.724],
                                    [0.696,  0.675,  0.654, 0.696],
                                    [0.731,  0.758,  0.738, 0.737]])],\
            ['Control','Control', array([0.625,  0.623,  0.61 ,  0.577, 0.615,
                                        0.642,  0.673, 0.682,  0.737, 0.704])],\
            ['Fast','Fast', array([0.718,  0.666, 0.727, 0.6, 0.578, 0.623])]
        ]}
        
        paired_field_exp = {'Treatment_to_Treatment':[\
            [('Control','Control'),('Fast','Fast'),\
                             array([[0.729,  0.8  ,  0.721, 0.765],
                                    [0.776,  0.744,  0.749, 0.677],
                                    [0.734,  0.777,  0.733, 0.724],
                                    [0.696,  0.675,  0.654, 0.696],
                                    [0.731,  0.758,  0.738, 0.737]])],\
            [('Control','Control'),('Control','Control'),\
                                 array([0.625,  0.623,  0.61 ,  0.577, 0.615,
                                        0.642,  0.673, 0.682,  0.737, 0.704])],\
            [('Fast','Fast'),('Fast','Fast'),\
                             array([0.718,  0.666, 0.727, 0.6, 0.578, 0.623])]
        ]}
        
        single_field_obs, paired_field_obs, dmat_obs = \
            group_distances(mapping_file=self.map_file,\
                dmatrix_file=self.dmat_file,\
                fields=['Treatment'],\
                dir_prefix=self.working_dir)
        
        self.assertEqual(single_field_exp,single_field_obs)
        self.assertEqual(paired_field_exp,paired_field_obs)        
        self.assertEqual(self.dmat,dmat_obs)
        
    def test_monte_carlo_group_distances(self):
        """monte_carlo_group_distances should return correct result.
        """
        mc_group_dist_path = self.working_dir+\
            'monte_carlo_group_distances/group_distances_Treatment.xls'
        monte_carlo_group_distances(mapping_file=self.map_file,\
                                    dmatrix_file=self.dmat_file,\
                                    prefs=PREFS,\
                                    dir_prefix=self.working_dir)
        obs_res = open(mc_group_dist_path,'U').readlines()
        exp_res = MONTE_CARLO_DISTANCES.split('\n')
        for obs, exp in zip(obs_res, exp_res):
            obs_fields = obs.split('\t')
            exp_fields = exp.split('\t')

            #Check first 8 fields should be identical from run to run.
            for i in range(8):
                self.assertEqual(obs_fields[i],exp_fields[i])

    def test_permute_for_monte_carlo(self):
        """permute_for_monte_carlo should return correct result.
        """
        obs = permute_for_monte_carlo(self.dmat)
        self.assertNotEqual(obs,self.dmat)
        self.assertEqual(len(obs),len(self.dmat))
        self.assertEqual(sorted(obs.flat),sorted(self.dmat.flat))
    
    def test_monte_carlo_group_distances_within_between(self):
        """monte_carlo_group_distances_within_between should return correct.
        """
        mc_group_dist_path = self.working_dir+\
            'monte_carlo_group_distances/group_distances_within_and_between.xls'
        monte_carlo_group_distances_within_between(\
            single_field=self.single_field_treatment,\
            paired_field=self.paired_field_treatment,\
            dmat=self.dmat,\
            dir_prefix=self.working_dir)
        obs_res = open(mc_group_dist_path,'U').readlines()
        exp_res = MONTE_CARLO_DISTANCES_WITHIN_BETWEEN.split('\n')
        for obs, exp in zip(obs_res, exp_res):
            obs_fields = obs.split('\t')
            exp_fields = exp.split('\t')
            #Check first 8 fields should be identical from run to run.
            for i in range(8):
                self.assertEqual(obs_fields[i],exp_fields[i])

    def test_get_random_dists(self):
        """get_random_dists should return correct result.
        """
        real_dists = [['first_a','second_a',[.1,.2,.3,.4,.5]],\
                      ['first_b','second_b',[.01,.02,.03,.04,.05]]]
        obs_dists = get_random_dists(real_dists, self.dmat, 2)
        exp_dists = [[['first_a','second_a',[.5,.1,.6,.01,.2]],\
               ['first_b','second_b',[.61,.32,.13,.94,.25]],\
               ['first_a','second_a',[.7,.02,.12,.40,.05]],\
               ['first_b','second_b',[.93,.62,.88,.41,.85]]]]
        for obs, exp in zip(obs_dists[0], exp_dists[0]):
            self.assertEqual(obs[:2], exp[:2])
            self.assertEqual(len(obs[2]),len(exp[2]))

    def test__make_histogram_filenames(self):
        """_make_histogram_filenames should return correct result.
        """
        distances = {'Distances1':[0,.5,.6,.7],\
                     'Distances2':[.3,.7,.9,.2,1.]}
        obs = _make_histogram_filenames(distances,self.histogram_dir)

        self.assertEqual(obs.keys(),distances.keys())
        for k,v in obs.items():
            exp_prefix = self.histogram_dir
            self.assertEquals(path.split(v)[0],exp_prefix)
            self.assertEquals(v[-4:],'.png')

    def test__make_relative_paths(self):
        """_make_relative_paths should return correct result.
        """
        label_to_path = {'first_path':'/path/to/file1.txt',\
                         'second_path':'/path/to/file2.txt'}
        prefix = '/path/'
        exp = {'first_path':'./to/file1.txt',\
               'second_path':'./to/file2.txt'}
        self.assertEqual(_make_relative_paths(label_to_path,prefix),exp)
            
    def test__make_random_filename(self):
        """_make_random_filename should return correct result.
        """
        base_dir = './'
        suffix = 'test_suffix'
        num_chars = 10
        obs = _make_random_filename(base_dir=base_dir,suffix=suffix,\
            num_chars=num_chars)

        self.assertEqual(len(obs),sum([len(base_dir),len(suffix),num_chars]))
        self.assertEqual(obs[:len(base_dir)],base_dir)
        self.assertEqual(obs[len(base_dir)+num_chars:],suffix)


DISTANCE_MATRIX_STRING = \
"""\tPC.354\tPC.355\tPC.356\tPC.481\tPC.593\tPC.607\tPC.634\tPC.635\tPC.636
PC.354\t0.0\t0.625\t0.623\t0.61\t0.577\t0.729\t0.8\t0.721\t0.765
PC.355\t0.625\t0.0\t0.615\t0.642\t0.673\t0.776\t0.744\t0.749\t0.677
PC.356\t0.623\t0.615\t0.0\t0.682\t0.737\t0.734\t0.777\t0.733\t0.724
PC.481\t0.61\t0.642\t0.682\t0.0\t0.704\t0.696\t0.675\t0.654\t0.696
PC.593\t0.577\t0.673\t0.737\t0.704\t0.0\t0.731\t0.758\t0.738\t0.737
PC.607\t0.729\t0.776\t0.734\t0.696\t0.731\t0.0\t0.718\t0.666\t0.727
PC.634\t0.8\t0.744\t0.777\t0.675\t0.758\t0.718\t0.0\t0.6\t0.578
PC.635\t0.721\t0.749\t0.733\t0.654\t0.738\t0.666\t0.6\t0.0\t0.623
PC.636\t0.765\t0.677\t0.724\t0.696\t0.737\t0.727\t0.578\t0.623\t0.0"""

MAPPING_STRING = \
"""#SampleID\tBarcodeSequence\tTreatment\tDOB
PC.354\tAGCACGAGCCTA\tControl\t20061218
PC.355\tAACTCGTCGATG\tControl\t20061218
PC.356\tACAGACCACTCA\tControl\t20061126
PC.481\tACCAGCGACTAG\tControl\t20070314
PC.593\tAGCAGCACTTGT\tControl\t20071210
PC.607\tAACTGTGCGTAC\tFast\t20071112
PC.634\tACAGAGTCGGCT\tFast\t20080116
PC.635\tACCGCAGAGTCA\tFast\t20080116
PC.636\tACGGTGAGTGTC\tFast\t20080116
"""

PREFS = {
'MONTE_CARLO_GROUP_DISTANCES': {'Treatment':10},
'FIELDS':['Treatment'],
}

DISTANCES_OUT = \
"""Control_to_Fast\t0.729\t0.8\t0.721\t0.765\t0.776\t0.744\t0.749\t0.677\t0.734\t0.777\t0.733\t0.724\t0.696\t0.675\t0.654\t0.696\t0.731\t0.758\t0.738\t0.737
Control_to_Control\t0.625\t0.623\t0.61\t0.577\t0.615\t0.642\t0.673\t0.682\t0.737\t0.704
Fast_to_Fast\t0.718\t0.666\t0.727\t0.6\t0.578\t0.623
"""

MONTE_CARLO_DISTANCES = \
"""Category_1a\tCategory_1b\tAvg\tCategory_2a\tCategory_2b\tAvg\tt\tp\tp_greater\tp_less\tIterations\nControl\tFast\t0.7307\tControl\tControl\t0.6488\t3.27735729274\t0.0060036701418\t0.0\t1.0\t10\nControl\tFast\t0.7307\tFast\tFast\t0.652\t2.4827593877\t0.0348333795055\t0.0\t1.0\t10\nControl\tControl\t0.6488\tFast\tFast\t0.652\t-0.11479781274\t0.910235587908\t0.6\t0.4\t10\n"""

MONTE_CARLO_DISTANCES_WITHIN_BETWEEN = \
"""Comparison\tCategory_1\tAvg\tComparison\tCategory_2\tAvg\tt\tp\tp_greater\tp_less\tIterations\nWithin\tTreatment\t0.65\tBetween\tTreatment\t0.7307\t-5.42842519819\t4.76810168062e-06\t1.0\t0.0\t10\nWithin\tTreatment\t0.65\tWithin\tAll_Fields\t0.65\t0.0\t1.0\t0.2\t0.8\t10\nBetween\tTreatment\t0.7307\tWithin\tAll_Fields\t0.65\t5.42842519819\t4.76810168062e-06\t0.0\t1.0\t10\n'"""

NAV_HTML = \
"""<td>\n    <div style="overflow:scroll;white-space:nowrap;width:300px;height: 400px;">\n    <p>\n<span class="normal">All_Within_Category_Grouped</span><br />\n<span class="smnorm"><input type="checkbox" id="check_Treatment_All_Within_Category_Distances"  onclick="visibilityAndOpacity(this, \'Treatment_All_Within_Category_Distances\')" />\n<a onmouseover="mouseoverVisible(\'Treatment_All_Within_Category_Distances\')"; onmouseout="mouseoverHidden(\'Treatment_All_Within_Category_Distances\')">Treatment_All_Within_Category_Distances</a></span><br />\n<span class="normal">All_Between_Category_Grouped</span><br />\n<span class="smnorm"><input type="checkbox" id="check_Treatment_All_Between_Category_Distances"  onclick="visibilityAndOpacity(this, \'Treatment_All_Between_Category_Distances\')" />\n<a onmouseover="mouseoverVisible(\'Treatment_All_Between_Category_Distances\')"; onmouseout="mouseoverHidden(\'Treatment_All_Between_Category_Distances\')">Treatment_All_Between_Category_Distances</a></span><br />\n<span class="normal">All_Between_Sample_Distances</span><br />\n<span class="smnorm"><input type="checkbox" id="check_All_Between_Sample_Distances" checked onclick="visibilityAndOpacity(this, \'All_Between_Sample_Distances\')" />\n<a onmouseover="mouseoverVisible(\'All_Between_Sample_Distances\')"; onmouseout="mouseoverHidden(\'All_Between_Sample_Distances\')">All_Between_Sample_Distances</a></span><br />\n<span class="normal">All_Within_And_Between_Fields</span><br />\n<span class="smnorm"><input type="checkbox" id="check_Within_All_Fields"  onclick="visibilityAndOpacity(this, \'Within_All_Fields\')" />\n<a onmouseover="mouseoverVisible(\'Within_All_Fields\')"; onmouseout="mouseoverHidden(\'Within_All_Fields\')">Within_All_Fields</a></span><br />\n<span class="normal">All_Category_Pairs</span><br />\n<span class="smnorm"><input type="checkbox" id="check_Treatment###FIELDDATA###Control_to_Control"  onclick="visibilityAndOpacity(this, \'Treatment###FIELDDATA###Control_to_Control\')" />\n<a onmouseover="mouseoverVisible(\'Treatment###FIELDDATA###Control_to_Control\')"; onmouseout="mouseoverHidden(\'Treatment###FIELDDATA###Control_to_Control\')">Treatment_Control_to_Control</a></span><br />\n<span class="smnorm"><input type="checkbox" id="check_Treatment###FIELDDATA###Control_to_Fast"  onclick="visibilityAndOpacity(this, \'Treatment###FIELDDATA###Control_to_Fast\')" />\n<a onmouseover="mouseoverVisible(\'Treatment###FIELDDATA###Control_to_Fast\')"; onmouseout="mouseoverHidden(\'Treatment###FIELDDATA###Control_to_Fast\')">Treatment_Control_to_Fast</a></span><br />\n<span class="smnorm"><input type="checkbox" id="check_Treatment###FIELDDATA###Fast_to_Fast"  onclick="visibilityAndOpacity(this, \'Treatment###FIELDDATA###Fast_to_Fast\')" />\n<a onmouseover="mouseoverVisible(\'Treatment###FIELDDATA###Fast_to_Fast\')"; onmouseout="mouseoverHidden(\'Treatment###FIELDDATA###Fast_to_Fast\')">Treatment_Fast_to_Fast</a></span><br />\n<span class="normal">All_Within_Categories</span><br />\n<span class="smnorm"><input type="checkbox" id="check_Treatment_Within_Control_Distances"  onclick="visibilityAndOpacity(this, \'Treatment_Within_Control_Distances\')" />\n<a onmouseover="mouseoverVisible(\'Treatment_Within_Control_Distances\')"; onmouseout="mouseoverHidden(\'Treatment_Within_Control_Distances\')">Treatment_Within_Control_Distances</a></span><br />\n<span class="smnorm"><input type="checkbox" id="check_Treatment_Within_Fast_Distances"  onclick="visibilityAndOpacity(this, \'Treatment_Within_Fast_Distances\')" />\n<a onmouseover="mouseoverVisible(\'Treatment_Within_Fast_Distances\')"; onmouseout="mouseoverHidden(\'Treatment_Within_Fast_Distances\')">Treatment_Within_Fast_Distances</a></span><br />\n    </p>\n    </div>\n    </td>\n\
"""

MAIN_HTML = \
"""
<html><head> <title>
QIIME - Distance Histograms
</title>
<script type="text/javascript" src="./js/histograms.js"></script>
 <style type="text/css">
.smnorm {color: blue; font-family:Arial,Verdana; font-size:10; font-weight: bold;}
.normal {color: black; font-family:Arial,Verdana; font-size:11; font-weight: bold;}

</style>
</head>
<body> 
<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>
<div>
    <table>
        <tr>
            
<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:visible;" id="All_Between_Sample_Distances" name="visible" src="/tmp/distance_histogram_tests/histograms/FSFRIojoGyfL2iGYVFbr.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="All_Between_Sample_Distances" name="hidden" src="/tmp/distance_histogram_tests/histograms/FSFRIojoGyfL2iGYVFbr.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="Treatment_Within_Fast_Distances" name="hidden" src="/tmp/distance_histogram_tests/histograms/6aMGfDaBtx1UctPtV4qT.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="Within_All_Fields" name="hidden" src="/tmp/distance_histogram_tests/histograms/uBnt1Qbg0qoasH8xCg5Q.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="Treatment###FIELDDATA###Fast_to_Fast" name="hidden" src="/tmp/distance_histogram_tests/histograms/YdQdIIROef1jixUaS3X4.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="Treatment###FIELDDATA###Control_to_Fast" name="hidden" src="/tmp/distance_histogram_tests/histograms/mPBMbyfSxunyeR2GSQpQ.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="Treatment_All_Between_Category_Distances" name="hidden" src="/tmp/distance_histogram_tests/histograms/3leAJFaXwrMqtJKgTm7v.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="Treatment_All_Within_Category_Distances" name="hidden" src="/tmp/distance_histogram_tests/histograms/JHmUx9dH2lmdmxPlDumP.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="Treatment###FIELDDATA###Control_to_Control" name="hidden" src="/tmp/distance_histogram_tests/histograms/wfy4pNiN0j7843Tawase.png" border="0"></td>

<td style="position:absolute;left:0;">
<img style="z-index:1; opacity:1.0;filter:alpha(opacity=100); visibility:hidden;" id="Treatment_Within_Control_Distances" name="hidden" src="/tmp/distance_histogram_tests/histograms/geDPwHcu38bQINLYappd.png" border="0"></td>
        </tr>
    </table>
</div>


<table style="position:absolute;left:600">
    <tr>
    <td>
    <div style="overflow:scroll;white-space:nowrap;width:300px;height: 400px;">
    <p>
<span class="normal">All_Within_Category_Grouped</span><br />
<span class="smnorm"><input type="checkbox" id="check_Treatment_All_Within_Category_Distances"  onclick="visibilityAndOpacity(this, 'Treatment_All_Within_Category_Distances')" />
<a onmouseover="mouseoverVisible('Treatment_All_Within_Category_Distances')"; onmouseout="mouseoverHidden('Treatment_All_Within_Category_Distances')">Treatment_All_Within_Category_Distances</a></span><br />
<span class="normal">All_Between_Category_Grouped</span><br />
<span class="smnorm"><input type="checkbox" id="check_Treatment_All_Between_Category_Distances"  onclick="visibilityAndOpacity(this, 'Treatment_All_Between_Category_Distances')" />
<a onmouseover="mouseoverVisible('Treatment_All_Between_Category_Distances')"; onmouseout="mouseoverHidden('Treatment_All_Between_Category_Distances')">Treatment_All_Between_Category_Distances</a></span><br />
<span class="normal">All_Between_Sample_Distances</span><br />
<span class="smnorm"><input type="checkbox" id="check_All_Between_Sample_Distances" checked onclick="visibilityAndOpacity(this, 'All_Between_Sample_Distances')" />
<a onmouseover="mouseoverVisible('All_Between_Sample_Distances')"; onmouseout="mouseoverHidden('All_Between_Sample_Distances')">All_Between_Sample_Distances</a></span><br />
<span class="normal">All_Within_And_Between_Fields</span><br />
<span class="smnorm"><input type="checkbox" id="check_Within_All_Fields"  onclick="visibilityAndOpacity(this, 'Within_All_Fields')" />
<a onmouseover="mouseoverVisible('Within_All_Fields')"; onmouseout="mouseoverHidden('Within_All_Fields')">Within_All_Fields</a></span><br />
<span class="normal">All_Category_Pairs</span><br />
<span class="smnorm"><input type="checkbox" id="check_Treatment###FIELDDATA###Control_to_Control"  onclick="visibilityAndOpacity(this, 'Treatment###FIELDDATA###Control_to_Control')" />
<a onmouseover="mouseoverVisible('Treatment###FIELDDATA###Control_to_Control')"; onmouseout="mouseoverHidden('Treatment###FIELDDATA###Control_to_Control')">Treatment_Control_to_Control</a></span><br />
<span class="smnorm"><input type="checkbox" id="check_Treatment###FIELDDATA###Control_to_Fast"  onclick="visibilityAndOpacity(this, 'Treatment###FIELDDATA###Control_to_Fast')" />
<a onmouseover="mouseoverVisible('Treatment###FIELDDATA###Control_to_Fast')"; onmouseout="mouseoverHidden('Treatment###FIELDDATA###Control_to_Fast')">Treatment_Control_to_Fast</a></span><br />
<span class="smnorm"><input type="checkbox" id="check_Treatment###FIELDDATA###Fast_to_Fast"  onclick="visibilityAndOpacity(this, 'Treatment###FIELDDATA###Fast_to_Fast')" />
<a onmouseover="mouseoverVisible('Treatment###FIELDDATA###Fast_to_Fast')"; onmouseout="mouseoverHidden('Treatment###FIELDDATA###Fast_to_Fast')">Treatment_Fast_to_Fast</a></span><br />
<span class="normal">All_Within_Categories</span><br />
<span class="smnorm"><input type="checkbox" id="check_Treatment_Within_Control_Distances"  onclick="visibilityAndOpacity(this, 'Treatment_Within_Control_Distances')" />
<a onmouseover="mouseoverVisible('Treatment_Within_Control_Distances')"; onmouseout="mouseoverHidden('Treatment_Within_Control_Distances')">Treatment_Within_Control_Distances</a></span><br />
<span class="smnorm"><input type="checkbox" id="check_Treatment_Within_Fast_Distances"  onclick="visibilityAndOpacity(this, 'Treatment_Within_Fast_Distances')" />
<a onmouseover="mouseoverVisible('Treatment_Within_Fast_Distances')"; onmouseout="mouseoverHidden('Treatment_Within_Fast_Distances')">Treatment_Within_Fast_Distances</a></span><br />
    </p>
    </div>
    </td>

    </tr>
</table>
"""

DATA_COLOR_ORDER = ['blue1', 'lime', 'red1', 'blue2', 'purple1', 'yellow1', \
    'green2', 'red2', 'teal1', 'purple', 'olive', 'silver', 'gray']

FIELD_TO_COLOR_PREFS = {'DOB': ({'20070314': ['PC.481'], '20071112': ['PC.607'], '20080116': ['PC.634', 'PC.635', 'PC.636'], '20061126': ['PC.356'], '20061218': ['PC.354', 'PC.355'], '20071210': ['PC.593']}, {'20070314': 'red1', '20071112': 'blue2', '20080116': 'yellow1', '20061126': 'blue1', '20061218': 'lime', '20071210': 'purple1'}, data_colors, DATA_COLOR_ORDER),'Treatment': ({'Control': ['PC.354', 'PC.355', 'PC.356', 'PC.481', 'PC.593'], 'Fast': ['PC.607', 'PC.634', 'PC.635', 'PC.636']}, {'Control': 'blue1', 'Fast': 'lime'}, data_colors, DATA_COLOR_ORDER), 'BarcodeSequence': ({'ACCAGCGACTAG': ['PC.481'], 'ACCGCAGAGTCA': ['PC.635'], 'AACTGTGCGTAC': ['PC.607'], 'AGCAGCACTTGT': ['PC.593'], 'ACAGAGTCGGCT': ['PC.634'], 'AACTCGTCGATG': ['PC.355'], 'ACGGTGAGTGTC': ['PC.636'], 'AGCACGAGCCTA': ['PC.354'], 'ACAGACCACTCA': ['PC.356']}, {'ACCAGCGACTAG': 'purple1', 'ACCGCAGAGTCA': 'yellow1', 'AACTGTGCGTAC': 'lime', 'ACAGACCACTCA': 'red1', 'ACAGAGTCGGCT': 'blue2', 'AACTCGTCGATG': 'blue1', 'ACGGTGAGTGTC': 'green2', 'AGCAGCACTTGT': 'teal1', 'AGCACGAGCCTA': 'red2'}, data_colors, DATA_COLOR_ORDER),'Description': ({'Fasting mouse, I.D. 607': ['PC.607'], 'Control mouse, I.D. 481': ['PC.481'], 'Control mouse, I.D. 593': ['PC.593'], 'Control mouse, I.D. 356': ['PC.356'], 'Control mouse, I.D. 354': ['PC.354'], 'Control mouse, I.D. 355': ['PC.355'], 'Fasting mouse, I.D. 634': ['PC.634'], 'Fasting mouse, I.D. 635': ['PC.635'], 'Fasting mouse, I.D. 636': ['PC.636']}, {'Fasting mouse, I.D. 607': 'yellow1', 'Control mouse, I.D. 481': 'blue2', 'Control mouse, I.D. 593': 'purple1', 'Control mouse, I.D. 356': 'red1', 'Control mouse, I.D. 354': 'blue1', 'Control mouse, I.D. 355': 'lime', 'Fasting mouse, I.D. 634': 'green2', 'Fasting mouse, I.D. 635': 'red2', 'Fasting mouse, I.D. 636': 'teal1'}, data_colors, DATA_COLOR_ORDER), 'SampleID': ({'PC.636': ['PC.636'], 'PC.355': ['PC.355'], 'PC.607': ['PC.607'], 'PC.634': ['PC.634'], 'PC.635': ['PC.635'], 'PC.593': ['PC.593'], 'PC.356': ['PC.356'], 'PC.481': ['PC.481'], 'PC.354': ['PC.354']}, {'PC.636': 'teal1', 'PC.355': 'lime', 'PC.607': 'yellow1', 'PC.634': 'green2', 'PC.635': 'red2', 'PC.593': 'purple1', 'PC.356': 'red1', 'PC.481': 'blue2', 'PC.354': 'blue1'}, data_colors, DATA_COLOR_ORDER)}

#run tests if called from command line
if __name__ == "__main__":
    main()