def view(args): g = load_from_fasta_tsv(args.fasta, args.edges, args.containment) # save_to_fasta_tsv(g, 'test.fasta', 'test.tsv', 'test.containment') # g = load_from_fasta_tsv('test.fasta', 'test.tsv', 'test.containment') if args.check_correctness: visualize_correctness(g) if args.vertex: print_vertex(g.vertex_from_id(args.vertex)) if args.edge: print_connection(g.get_edge(args.edge)) if args.dot: to_graphviz_dot(g, args.dot) if args.gfa: save_bandage_gfa(g, args.gfa)
def inspect_new_edges(g): for e in g.edges: v1, v2 = e.v1, e.v2 contractable = False if e.connection[v1] == 'H' and len(v1.head_edges) == 1: if e.connection[v2] == 'H' and len(v2.head_edges) == 1: contractable = True elif e.connection[v2] == 'T' and len(v2.tail_edges) == 1: contractable = True elif e.connection[v1] == 'T' and len(v1.tail_edges) == 1: if e.connection[v2] == 'H' and len(v2.head_edges) == 1: contractable = True elif e.connection[v2] == 'T' and len(v2.tail_edges) == 1: contractable = True print print e.id, v1.id, v2.id, e.connection[v1], e.connection[v2], contractable print_vertex(v1) print_vertex(v2)
def inspect_new_edges(g): for e in g.edges: v1, v2 = e.v1, e.v2 contractable = False if e.connection[v1] == 'H' and len(v1.head_edges) == 1: if e.connection[v2] == 'H' and len(v2.head_edges) == 1: contractable = True elif e.connection[v2] == 'T' and len(v2.tail_edges) == 1: contractable = True elif e.connection[v1] == 'T' and len(v1.tail_edges) == 1: if e.connection[v2] == 'H' and len(v2.head_edges) == 1: contractable = True elif e.connection[v2] == 'T' and len(v2.tail_edges) == 1: contractable = True print print e.id, v1.id, v2.id, e.connection[v1], e.connection[ v2], contractable print_vertex(v1) print_vertex(v2)