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 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)
