def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) data = {} mapping, headers, comments = get_map(opts, data) mapping_headers_to_use = opts.mapping_headers_to_use background_color = opts.background_color monte_carlo_dist = opts.monte_carlo_dist ball_scale = opts.ball_scale arrow_line_color = opts.arrow_line_color arrow_head_color = opts.arrow_head_color taxonomy_count_file = opts.input_taxa_file if taxonomy_count_file: try: counts_f = open(taxonomy_count_file, 'U').readlines() _, taxa_ids, _ = \ parse_taxa_summary_table(counts_f) except (TypeError, IOError): raise ValueError('Summarized taxa file could not be parsed.') else: taxa_ids = None out = build_prefs_string(mapping_headers_to_use, background_color, monte_carlo_dist, headers, taxa_ids, ball_scale, arrow_line_color, arrow_head_color) f = open(opts.output_fp, 'w') f.write(out) f.close()
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) data={} mapping,headers,comments = get_map(opts, data) mapping_headers_to_use=opts.mapping_headers_to_use background_color=opts.background_color monte_carlo_dist=opts.monte_carlo_dist ball_scale=opts.ball_scale arrow_line_color=opts.arrow_line_color arrow_head_color=opts.arrow_head_color taxonomy_count_file = opts.input_taxa_file if taxonomy_count_file: try: counts_f = open(taxonomy_count_file, 'U').readlines() _, taxa_ids, _ = \ parse_taxa_summary_table(counts_f) except (TypeError, IOError): raise ValueError, 'Summarized taxa file could not be parsed.' else: taxa_ids=None out = build_prefs_string(mapping_headers_to_use, background_color, \ monte_carlo_dist, headers, taxa_ids, \ ball_scale, arrow_line_color, arrow_head_color) f = open(opts.output_fp,'w') f.write(out) f.close()
def test_build_prefs_string(self): """build_prefs_string should return a properly formatted prefs string. """ # Try with correctly formatted color_by_string mapping_headers_to_use = "First,Second" background_color = "black" monte_carlo_dist = 10 otu_ids = ["Root;Bacteria"] headers = ["First", "Second"] ball_size = 2.5 arrow_head_color = "red" arrow_line_color = "white" exp_string = """{\n'background_color':'black',\n\n'sample_coloring':\n\t{\n\t\t'First':\n\t\t{\n\t\t\t'column':'First',\n\t\t\t'colors':(('red',(0,100,100)),('blue',(240,100,100)))\n\t\t},\n\t\t'Second':\n\t\t{\n\t\t\t'column':'Second',\n\t\t\t'colors':(('red',(0,100,100)),('blue',(240,100,100)))\n\t\t}\n\t},\n'MONTE_CARLO_GROUP_DISTANCES':\n\t{\n\t\t'First': 10,\n\t\t'Second': 10\n\t},\n'FIELDS':\n\t[\n\t\t'Second',\n\t\t'First'\n\t],\n'taxonomy_coloring':\n\t{\n\t\t'Level_1':\n\t\t{\n\t\t\t'column':'1',\n\t\t\t'colors':\n\t\t\t{\n\t\t\t\t'Root;Bacteria':('red0',(0,100,100))\n\t\t\t}\n\t\t}\n\t},\n'ball_scale':'2.500000',\n'arrow_line_color':'white',\n'arrow_head_color':'red'\n}""" obs_string = build_prefs_string( mapping_headers_to_use, background_color, monte_carlo_dist, headers, otu_ids, ball_size, arrow_line_color, arrow_head_color, ) self.assertEqual(obs_string, exp_string)
def test_build_prefs_string(self): """build_prefs_string should return a properly formatted prefs string. """ #Try with correctly formatted color_by_string mapping_headers_to_use='First,Second' background_color='black' monte_carlo_dist=10 otu_ids=['Root;Bacteria'] headers=['First','Second'] exp_string = \ """{\n'background_color':'black',\n\n'sample_coloring':\n\t{\n\t\t'First':\n\t\t{\n\t\t\t'column':'First',\n\t\t\t'colors':(('red',(0,100,100)),('blue',(240,100,100)))\n\t\t},\n\t\t'Second':\n\t\t{\n\t\t\t'column':'Second',\n\t\t\t'colors':(('red',(0,100,100)),('blue',(240,100,100)))\n\t\t}\n\t},\n'MONTE_CARLO_GROUP_DISTANCES':\n\t{\n\t\t'First': 10,\n\t\t'Second': 10\n\t},\n'FIELDS':\n\t[\n\t\t'Second',\n\t\t'First'\n\t],\n'taxonomy_coloring':\n\t{\n\t\t'Level_1':\n\t\t{\n\t\t\t'column':'1',\n\t\t\t'colors':\n\t\t\t{\n\t\t\t\t'Root;Bacteria':('red0',(0,100,100))\n\t\t\t}\n\t\t}\n\t}\n}""" obs_string = build_prefs_string(mapping_headers_to_use, \ background_color, monte_carlo_dist, headers, otu_ids) self.assertEqual(obs_string,exp_string)