def test_convert_all():
network = kegg_tools.pathway_id_to_network('hsa00040')
network = convert_all(network, verbose=True)
print(sorted(network.nodes))
ans = {
'chemName': 'D-Ribulose 5-phosphate',
'keggName': 'C00199',
'hmdbNames': 'HMDB0000618',
'databaseSource': 'KEGG',
'speciesType': 'compound'
}
print(network.node['HMDB0000618'])
print(network.node['DHDH'])
def download_kegg(species='hsa', verbose=False):
"""
Downloads every KEGG pathway to provided directory
"""
if species == 'hsa':
from magine.mappings.maps import convert_all
kegg.organism = species
list_of_kegg_pathways = [i[5:] for i in kegg.pathwayIds]
if verbose:
print("Number of pathways = {}".format(len(list_of_kegg_pathways)))
# keys are KEGG pathways ids, values are kegg pathways
kegg_dict = dict()
for pathway_id in list_of_kegg_pathways:
pathway = kegg.get(pathway_id, "kgml")
if pathway == 404:
print("%s ended with 404 error" % pathway_id)
continue
graph, pathway_name = kgml_to_nx(pathway, species=species)
if species == 'hsa':
graph = convert_all(graph, species)
kegg_dict[pathway_id] = graph
if verbose:
print('{} has {} nodes and {} edges'.format(pathway_name,
len(graph.nodes),
len(graph.edges)))
# create a dictionary mapping species to pathways
node_to_path = dict()
for i in kegg_dict:
for node in kegg_dict[i].nodes:
if node not in node_to_path:
node_to_path[node] = set()
node_to_path[node].add(i)
# save kegg pathway its to networks
n = '{}_kegg_path_ids_to_networks.p.gz'.format(species)
save_path_id_to_graph = os.path.join(network_data_dir, n)
save_gzip_pickle(save_path_id_to_graph, kegg_dict)
# save nodes to pathways
n = '{}_kegg_node_to_pathway.p.gz'.format(species)
save_node_to_path = os.path.join(network_data_dir, n)
save_gzip_pickle(save_node_to_path, node_to_path)
def load_all_of_kegg(species='hsa', fresh_download=False, verbose=False):
"""
Combines all KEGG pathways into a single network
Parameters
----------
species : species
Default 'hsa'
fresh_download : bool
Download kegg new
verbose : bool
Returns
-------
"""
p_name = os.path.join(network_data_dir,
'{}_all_of_kegg.p.gz'.format(species))
# load in network if it exists
if os.path.exists(p_name) and not fresh_download:
if verbose:
print('Reading in KEGG network')
all_of_kegg = nx.read_gpickle(p_name)
else:
# create the network
path_to_graph, _ = load_kegg_mappings(species,
verbose=verbose,
fresh_download=fresh_download)
# merge into single networks
all_of_kegg = utils.compose_all(path_to_graph.values())
# relabel notes
if species == 'hsa':
from magine.mappings.maps import convert_all
all_of_kegg = convert_all(all_of_kegg, species=species)
# save network
nx.write_gpickle(all_of_kegg, p_name)
print("KEGG network {} nodes and {} edges".format(len(all_of_kegg.nodes),
len(all_of_kegg.edges)))
return all_of_kegg
def test_convert_all():
network = kegg_tools.pathway_id_to_network('hsa00040')
convert_all(network, verbose=True)