def retrieve_components(graph_dict, tumor_type, all_cogs,
radius, signif_res_neighbours):
"""Get the connected components and format the output."""
#inv_signif_struct_info = {v: k for k, v in signif_struct_info.items()}
ttype_output = []
#neighbours = pstruct.find_neighbors(all_cogs, radius)
for mystruct in graph_dict:
g = graph_dict[mystruct]
components = graph.connected_components(g)
added_components = components
"""
added_components = []
for cluster in components:
neighbours_in_cluster = set()
for res in cluster:
if res in signif_res_neighbours:
neighbours_in_cluster |= signif_res_neighbours[res]
added_components.append(cluster | neighbours_in_cluster)
"""
#print added_components
tmp = [mystruct, tumor_type]
for component in added_components:
format_str = ';'.join('{0}:{1}:{2}'.format(n[0], n[1], n[2]) for n in component)
tmp.append(format_str)
ttype_output.append(tmp)
return ttype_output
def retrieve_components(graph_dict, tumor_type):
"""Get the connected components and format the output."""
ttype_output = []
for mygene in graph_dict:
g = graph_dict[mygene]
components = graph.connected_components(g)
tmp = [mygene, tumor_type]
for component in components:
format_str = ';'.join('{0}:{1}'.format(n[1], n[2]) for n in component)
tmp.append(format_str)
ttype_output.append(tmp)
return ttype_output
def retrieve_components(graph_dict, tumor_type):
"""Get the connected components and format the output."""
ttype_output = []
for mygene in graph_dict:
g = graph_dict[mygene]
components = graph.connected_components(g)
tmp = [mygene, tumor_type]
for component in components:
format_str = ';'.join('{0}:{1}'.format(n[1], n[2])
for n in component)
tmp.append(format_str)
ttype_output.append(tmp)
return ttype_output
