def test_render_latex_macro(self):
# Sets up variable for testing
known_macro = '\\def\\TaxonomyA{Genus \\textit{Escherichia}}\n'\
'\\def\\DoctorA{10.00%}\n'\
'\\def\\HumansA{1.00%}\n'\
'\\def\\FoldA{10}\n'\
'\\def\\TaxonomyB{\\textit{Escherichia coli}}\n'\
'\\def\\DoctorB{0.10%}\n'\
'\\def\\HumansB{1.00%}\n'\
'\\def\\FoldB{0.10}'
# Calculates test variable
test_macro = generate_latex_macro(self.test_table, self.header)
# Checks the outputs match
self.assertEqual(known_macro, test_macro)
def main(taxa_table, output_dir, samples_to_analyze = None):
"""Creates LaTeX formatted significant OTU lists
INPUTS:
taxa -- a numpy vector with greengenes taxonomy strings
tax_table -- a numpy array with the relative frequencies of taxonomies
(rows) for each give sample (column)
samples_to_analyze -- a numpy vector of sample ids associated with the
tax_table values
output_dir -- a directory where the final files should be saved.
samples_to_analyze -- a list of samples_to_analyze which should be used
to generate data. If this is left empty, all the samples in
the table will be used.
OUTPUTS:
Generates text files containing LaTex encoded strings which creates a
LaTeX macro dictionary with the information for creating a table of most
abundant taxa, most enriched taxa, and rare and unique taxa. Rare
defined as present in less than 10% of the total population. The unique
taxa are bolded in the lists.
"""
# Sets table constants
RARE_THRESHHOLD = 0.1
RENDERING = "LATEX"
FORMAT_SIGNIFIGANCE = ['%1.1f', "%1.2f", "%i", "SKIP"]
SIGNIFIGANCE_HUNDRED = [True, True, False, False]
DUMMY = ['','','','']
COUNT = [0, 1, 2, 3, 4, 5, 6, 7]
FORMAT_ABUNDANCE = ["%1.1f"]
ABUNDANCE_HUNDRED = [True]
MACRO_CATS_SIGNIFICANCE = ['enrichTaxon','enrichSampl', 'enrichPopul',
'enrichFoldd']
MACRO_CATS_ABUNDANCE = ['abundTaxon', 'abundSampl']
FILE_PRECURSER = 'macros_'
FILE_EXTENSION = '.tex'
# Number of taxa shown is an indexing value, it is one less than what is
# actually shown.
NUMBER_OF_TAXA_SHOWN = 5
# Builds the the taxomnomy tree for the table and identifies the
# rare/unique taxa in each sample
tree, all_taxa = build_tree_from_taxontable(taxa_table)
# Sets up samples for which tables are being generated
if not samples_to_analyze == None:
samples_to_test = samples_to_analyze
else:
samples_to_test = all_taxa.keys()
if samples_to_test:
samples_to_test = set(samples_to_test)
tmp = {k:v for k,v in all_taxa.items() if k in samples_to_test}
all_taxa = tmp
if not samples_to_test:
raise ValueError, "No samples!"
# Generates lists and tables for each sample
for samp, filtered_table, rare, unique in sample_rare_unique(tree, \
taxa_table, all_taxa, RARE_THRESHHOLD):
filtered_table = filtered_table.filterObservations(lambda v,i,md:\
v.sum() > 0)
# Gets sample information for other samples
taxa = filtered_table.ObservationIds
population = array([filtered_table.observationData(i) for i in \
filtered_table.ObservationIds])
sample_position = filtered_table.getSampleIndex(samp)
sample = filtered_table.sampleData(samp)
print samp, sum(sample > 0)
population = delete(population, sample_position, 1)
# Converts the lists into greengenes strings for later processing
greengenes_rare = []
greengenes_unique = []
for taxon in rare:
greengenes_rare.append('; '.join(taxon))
for taxon in unique:
greengenes_unique.append('; '.join(taxon))
# Formats the rare and unique lists
rare_format = []
rare_combined = []
for taxon in greengenes_unique:
rare_combined.append(taxon)
rare_format.append('COLOR')
for taxon in greengenes_rare:
rare_combined.append(taxon)
rare_format.append('REG')
number_rare_tax = len(rare_combined)
num_rare = len(rare)
num_unique = len(unique)
rare_formatted = convert_taxa_to_list(rare_combined[0:NUMBER_OF_TAXA_SHOWN],
tax_format = rare_format,
render_mode = RENDERING,
comma = True)
if num_unique > 0:
unique_string = ' and \\textcolor{red}{%i unique}' % num_unique
else:
unique_string = ''
if number_rare_tax == 0:
rare_formatted = "There were no rare or unique taxa found in "\
"your sample."
elif 0 < number_rare_tax <= NUMBER_OF_TAXA_SHOWN:
rare_formatted = 'Your sample contained the following rare %s '\
'taxa: %s.' % (unique_string, rare_formatted)
else:
rare_formatted = 'Your sample contained %i rare and %s taxa, '\
'including the following: %s.' \
% (num_rare, unique_string,
rare_formatted)
# Calculates abundance rank
(abundance) = calculate_abundance(sample, taxa,
abundance_threshhold = 1)
# Generates formatted abundance table
formatted_abundance = convert_taxa(abundance[0:NUMBER_OF_TAXA_SHOWN],
formatting_keys = FORMAT_ABUNDANCE,
hundredx = ABUNDANCE_HUNDRED)
abundance_formatted = generate_latex_macro(formatted_abundance, \
categories = MACRO_CATS_ABUNDANCE)
(high, low) = calculate_tax_rank_1(sample = sample,
population = population,
taxa = taxa,
critical_value = 0.05)
if len(high) < NUMBER_OF_TAXA_SHOWN:
# Formats the known high taxa
formatted_high = convert_taxa(high[0:NUMBER_OF_TAXA_SHOWN],
formatting_keys = FORMAT_SIGNIFIGANCE,
hundredx = SIGNIFIGANCE_HUNDRED)
# Adds the dummy list to the end
for idx in COUNT:
if idx == (NUMBER_OF_TAXA_SHOWN - len(high)):
break
formatted_high.append(DUMMY)
high_formatted = generate_latex_macro(formatted_high, \
categories = MACRO_CATS_SIGNIFICANCE)
else:
formatted_high = convert_taxa(high[0:NUMBER_OF_TAXA_SHOWN],
formatting_keys = FORMAT_SIGNIFIGANCE,
hundredx = SIGNIFIGANCE_HUNDRED)
high_formatted = generate_latex_macro(formatted_high, \
categories = MACRO_CATS_SIGNIFICANCE)
file_name = pjoin(output_dir, '%s%s%s' % (FILE_PRECURSER, samp,
FILE_EXTENSION))
# Saves the file
file_for_editing = open(file_name, 'w')
# file_for_editing.write('% Participant Name\n\\def\\yourname'\
# '{Michael Pollan or longer name}\n\n')
file_for_editing.write('%% Abundance Table\n%s\n\n\n' \
% abundance_formatted)
file_for_editing.write('%% Enrichment Table\n%s\n\n\n' \
% high_formatted)
file_for_editing.write('%% Rare List\n\\def\\rareList{%s}\n' \
% rare_formatted)
file_for_editing.close()