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)
