def test_12_generate_functions_taxonomy_stamp_input(self):
for sample_id in self.project.list_samples():
self.project.import_reads_json(sample_id, self.project.ENDS)
metrics = 'efpkg'
# metrics = 'fragmentcount'
scores = get_function_taxonomy_scores(self.project,metrics=metrics)
generate_functions_taxonomy_stamp_input(self.project, scores, metrics)
def test_5_generate_functions_samples_xlsx(self):
for sample_id in self.project.list_samples():
self.project.import_reads_json(sample_id, self.project.ENDS)
metrics = 'efpkg'
rank = 'phylum'
scores = get_function_taxonomy_scores(self.project, metrics=metrics)
generate_sample_taxonomy_function_xlsx(self.project,
scores,
metrics=metrics,
rank = rank)
self.assertTrue(len(scores) > 0)
def test_0320_convert_profile_into_score_df(self):
self.project.import_reads_json(sample_id, ENDS)
scores = get_function_taxonomy_scores(self.project,
sample_id=sample_id,
metric='fpk')
sample_scores_taxonomy = slice_function_taxonomy_scores(
scores, sample_id)
taxonomy_profile = TaxonomyProfile()
taxonomy_profile.make_function_taxonomy_profile(
self.project.taxonomy_data, sample_scores_taxonomy)
result = taxonomy_profile.convert_profile_into_score_df(metric='fpk')
self.assertEqual(result.iloc[0][1], 'root')
self.assertEqual(result.iloc[1][0], 'superkingdom')
def test_0290_stringify_node(self):
self.project.import_reads_json(sample_id, ENDS)
scores = get_function_taxonomy_scores(self.project,
sample_id=sample_id,
metric='fpk')
sample_scores_taxonomy = slice_function_taxonomy_scores(
scores, sample_id)
taxonomy_profile = TaxonomyProfile()
taxonomy_profile.make_function_taxonomy_profile(
self.project.taxonomy_data, sample_scores_taxonomy)
self.assertEqual(
taxonomy_profile.stringify_node('118883', 0),
"118883\tfamily\tSulfolobaceae\tParent:2281\tChildren:None\tUreC:{'count': 1.0, 'hit_count': 1.0"
", 'identity': 68.8, 'fpk': 0.5984440454817475}\n")
def test_0330_convert_node_into_dict(self):
self.project.import_reads_json(sample_id, ENDS)
scores = get_function_taxonomy_scores(self.project,
sample_id=sample_id,
metric='fpk')
sample_scores_taxonomy = slice_function_taxonomy_scores(
scores, sample_id)
taxonomy_profile = TaxonomyProfile()
taxonomy_profile.make_function_taxonomy_profile(
self.project.taxonomy_data, sample_scores_taxonomy)
result, attributes = taxonomy_profile.convert_node_into_values_dict(
'118883', ['UreC', 'UreA'], 1, metric='fpk')
self.assertEqual(result[1][('', 'Taxon name')], 'Sulfolobaceae')
self.assertEqual(result[1][('UreC', 'fpk')], 0.5984440454817475)
self.assertEqual(result[1][('UreA', 'fpk')], 0.0)
self.assertEqual(attributes['UreC']['fpk'], 0.5984440454817475)
self.assertNotIn('UreA', attributes.keys())
def test_collect_taxonomic_data(self):
print ('Load project from JSON')
sample_id = 'FW306-ZV-1'
metrics = 'efpkg'
self.project.import_reads_json(sample_id, ENDS)
sample_scores = get_function_taxonomy_scores(self.project, sample_id = sample_id, metrics = metrics)# autovivify(2, float)
with open('sample1_taxonomy_scores.tsv', 'w') as of:
of.write('Taxonomy_ID\tFunction_ID\tScore\n')
for taxonomy_id in sorted(sample_scores.keys()):
for function_id in sorted(sample_scores[taxonomy_id].keys()):
of.write('\t'.join([taxonomy_id,function_id,str(sample_scores[taxonomy_id][function_id][sample_id][metrics])]) + '\n')
of.close()
self.assertEqual(len(self.project.samples), 6)
def test_0270_make_function_taxonomy_profile(self):
self.project.import_reads_json(sample_id, ENDS)
scores = get_function_taxonomy_scores(self.project,
sample_id=sample_id,
metric='fpk')
sample_scores_taxonomy = slice_function_taxonomy_scores(
scores, sample_id)
taxonomy_profile = TaxonomyProfile()
taxonomy_profile.make_function_taxonomy_profile(
self.project.taxonomy_data, sample_scores_taxonomy)
print(taxonomy_profile)
self.assertEqual(len(taxonomy_profile.tree.data), 22)
self.assertEqual(
taxonomy_profile.tree.data[ROOT_TAXONOMY_ID].attributes['NirK']
['count'], 1.0)
self.assertEqual(
taxonomy_profile.tree.data[ROOT_TAXONOMY_ID].attributes['UreA']
['count'], 3.0)
self.assertEqual(
taxonomy_profile.tree.data['118883'].attributes['UreC']['count'],
1.0)
