def search_orthologs_from_pangenome(self, token, ref, query, sort_by,
start, limit, num_found):
search_object = 'orthologs'
info_included = [
'id', 'type', 'function', 'md5', 'protein_translation', 'orthologs'
]
table_indexer = TableIndexer(token, self.ws_url)
ret = table_indexer.run_search(ref, self.pangenome_index_dir,
self.ORTHOLOGS_SUFFIX, search_object,
info_included, query, sort_by, start,
limit, num_found, self.debug)
for orthologs in ret['orthologs']:
orthologs_string = orthologs['orthologs']
if orthologs_string:
orthologs['orthologs'] = list(eval(orthologs_string))
if not isinstance(orthologs['orthologs'][0], list):
orthologs['orthologs'] = [orthologs['orthologs']]
ws = Workspace(self.ws_url, token=token)
genome_feature_function_map = {}
for orthologs in ret['orthologs']:
for orthologs_obj in orthologs['orthologs']:
gene_id = orthologs_obj[0]
if gene_id in genome_feature_function_map:
orthologs_obj.append(
genome_feature_function_map.get(gene_id))
else:
included = ["/features/[*]/function", "/features/[*]/id"]
object_info = ws.get_objects2({
'objects': [{
'ref': orthologs_obj[2],
'included': included
}]
})['data'][0]['data']
map(
lambda feature: genome_feature_function_map.update(
{feature.get('id'): feature.get('function')}),
object_info['features'])
orthologs_obj.append(
genome_feature_function_map.get(gene_id))
return ret
def search_comparison_genome_from_comparison_genome(
self, token, ref, query, sort_by, start, limit, num_found):
search_object = 'genomes'
info_included = [
'id', 'genome_ref', 'genome_similarity', 'name', 'taxonomy',
'features', 'families', 'functions'
]
table_indexer = TableIndexer(token, self.ws_url)
ret = table_indexer.run_search(ref, self.comparison_genome_index_dir,
self.COMPARISON_GENOMES_SUFFIX,
search_object, info_included, query,
sort_by, start, limit, num_found,
self.debug)
for genome in ret['genomes']:
if genome['genome_similarity']:
genome['genome_similarity'] = eval(genome['genome_similarity'])
return ret
def search_functions_from_comparison_genome(self, token, ref, query,
sort_by, start, limit,
num_found):
search_object = 'functions'
info_included = [
'core', 'genome_features', 'id', 'reactions', 'subsystem',
'primclass', 'subclass', 'number_genomes', 'fraction_genomes',
'fraction_consistent_families', 'most_consistent_family'
]
table_indexer = TableIndexer(token, self.ws_url)
ret = table_indexer.run_search(ref, self.comparison_genome_index_dir,
self.FUNCTIONS_SUFFIX, search_object,
info_included, query, sort_by, start,
limit, num_found, self.debug)
for function in ret['functions']:
if function['genome_features']:
function['genome_features'] = eval(function['genome_features'])
return ret
def search_families_from_comparison_genome(self, token, ref, query,
sort_by, start, limit,
num_found):
search_object = 'families'
info_included = [
'core', 'genome_features', 'id', 'type', 'protein_translation',
'number_genomes', 'fraction_genomes',
'fraction_consistent_annotations', 'most_consistent_role'
]
table_indexer = TableIndexer(token, self.ws_url)
ret = table_indexer.run_search(ref, self.comparison_genome_index_dir,
self.FAMILIES_SUFFIX, search_object,
info_included, query, sort_by, start,
limit, num_found, self.debug)
for family in ret['families']:
if family['genome_features']:
family['genome_features'] = eval(family['genome_features'])
return ret