def taxonomy_color_prefs_and_map_data_from_options(options):
"""Returns color prefs and counts data based on options.
counts data is any file in a format that can be parsed by parse_otu_table
"""
data = {}
data['counts'] = {}
taxonomy_levels = []
#need to set some other way from sample ids
#Determine which mapping headers to color by, if none given, color by \
#Sample ID's
taxonomy_count_files = options.counts_fname
for f in taxonomy_count_files:
try:
counts_f = open(f, 'U').readlines()
except (TypeError, IOError):
raise MissingFileError, 'Counts file required for this analysis'
sample_ids, otu_ids, otu_table = \
parse_taxa_summary_table(counts_f)
data['counts'][f] = (sample_ids, otu_ids, otu_table)
level = max([len(t.split(';')) - 1 for t in otu_ids])
taxonomy_levels.append(str(level))
if options.prefs_path:
prefs = eval(open(options.prefs_path, 'U').read())
color_prefs=taxonomy_process_prefs(taxonomy_levels, \
prefs['taxonomy_coloring'])
if prefs.has_key('background_color'):
background_color= prefs['background_color']
else:
background_color='black'
else:
background_color='black'
color_prefs=taxonomy_process_prefs(taxonomy_levels, None)
if options.prefs_path and options.background_color:
background_color=options.background_color
elif options.background_color:
background_color=options.background_color
if background_color=='black':
label_color='white'
else:
label_color='black'
return color_prefs,data,background_color,label_color
def taxonomy_color_prefs_and_map_data_from_options(options):
"""Returns color prefs and counts data based on options.
counts data is any file in a format that can be parsed by parse_otu_table
"""
data = {}
data["counts"] = {}
taxonomy_levels = []
# need to set some other way from sample ids
# Determine which mapping headers to color by, if none given, color by \
# Sample ID's
taxonomy_count_files = options.counts_fname
for f in taxonomy_count_files:
try:
counts_f = open(f, "U").readlines()
except (TypeError, IOError):
raise MissingFileError("Counts file required for this analysis")
sample_ids, otu_ids, otu_table = parse_taxa_summary_table(counts_f)
data["counts"][f] = (sample_ids, otu_ids, otu_table)
level = max([len(t.split(";")) - 1 for t in otu_ids])
taxonomy_levels.append(str(level))
if options.prefs_path:
prefs = eval(open(options.prefs_path, "U").read())
color_prefs = taxonomy_process_prefs(taxonomy_levels, prefs["taxonomy_coloring"])
if "background_color" in prefs:
background_color = prefs["background_color"]
else:
background_color = "black"
else:
background_color = "black"
color_prefs = taxonomy_process_prefs(taxonomy_levels, None)
if options.prefs_path and options.background_color:
background_color = options.background_color
elif options.background_color:
background_color = options.background_color
if background_color == "black":
label_color = "white"
else:
label_color = "black"
return color_prefs, data, background_color, label_color