def save_colored_insert_overlap_graph(graph_file, scaffolds,
scaffolds_refine, out_file):
graph = ar._load_dot(graph_file)
fout = open(out_file, "w")
main_strand = set()
all_contigs = set()
for scf in scaffolds:
main_strand |= set(map(lambda s: str(s), scf.contigs))
all_contigs |= set(map(lambda s: s.name, scf.contigs))
refine_contigs = set()
for scf in scaffolds_refine:
for cont in scf.contigs:
if str(cont) not in main_strand:
refine_contigs.add(str(cont))
fout.write("digraph {\n")
for node in graph.nodes_iter():
if str(node) in main_strand:
fout.write("\"{0}\" [style=filled, fillcolor=red];\n"
.format(node))
elif str(node)[1:] in all_contigs:
fout.write("\"{0}\" [style=filled, fillcolor=blue];\n"
.format(node))
elif str(node) in refine_contigs:
fout.write("\"{0}\" [style=filled, fillcolor=yellow];\n"
.format(node))
for u, v in graph.edges_iter():
fout.write("\"{0}\" -> \"{1}\";\n".format(u, v))
fout.write("}")
fout.close()
def save_distance_overlap_graph(graph_file, scaffolds_in, output_file):
max_path_len = 2 * config.ASSEMBLY_MAX_PATH_LEN
graph, edges = ar._load_dot(graph_file)
ordered_contigs = set()
fout = open(output_file, "w")
fout.write("digraph {\n")
for scf in scaffolds_in:
for cont in scf.contigs:
fout.write("{0} -> {1} [label=\"{2}\", color=\"red\"];\n"
.format(edges[str(cont)].start,
edges[str(cont)].end, str(cont)))
ordered_contigs.add(str(cont))
mark = set()
for scf in scaffolds_in:
for prev_cont, new_cont in zip(scf.contigs[:-1], scf.contigs[1:]):
try:
src = edges[str(prev_cont)].end
dst = edges[str(new_cont)].start
except KeyError:
logger.debug("contigs are not in the graph")
return None
if src != dst and nx.has_path(graph, src, dst):
paths = [p for p in nx.all_shortest_paths(graph, src, dst)]
path = paths[0]
is_good = True
for p_start, p_end in zip(path[:-1], path[1:]):
found_edge = None
for edge_id, edge in edges.items():
if edge == Edge(p_start, p_end):
found_edge = edge_id
break
assert found_edge
if (found_edge in ordered_contigs and
found_edge != str(prev_cont) and
str(new_cont) != found_edge):
is_good = False
break
if (is_good and len(path) <= 2 * max_path_len and
len(path) > 1 and (src, dst) not in mark):
mark.add((src, dst))
fout.write("{0} -> {1} [label=\"{2}\"];\n"
.format(src, dst, len(path) - 1))
fout.write("}")
fout.close()
def save_compress_overlap_graph(graph_file, scaffolds_in, output_file):
graph, edges = ar._load_dot(graph_file)
graph = nx.DiGraph(graph)
ordered_contigs = set()
all_contigs = set()
for scf in scaffolds_in:
for cont in scf.contigs:
ordered_contigs.add(str(cont))
all_contigs.add(cont.name)
fout = open(output_file, "w")
fout.write("digraph {\n")
is_change = True
while is_change:
is_change = False
for v1, v2, labels in graph.edges_iter(data=True):
if (labels["label"] not in ordered_contigs and
labels["label"][1:] not in all_contigs):
is_good = True
for y in graph.neighbors(v2):
if (graph[v2][y]["label"] in ordered_contigs or
graph[v2][y]["label"][1:] in all_contigs or y == v1):
is_good = False
if is_good:
is_change = True
graph.remove_edge(v1, v2)
for y in graph.neighbors(v2):
graph.add_edge(v1, y, label=graph[v2][y]["label"])
graph.remove_edge(v2, y)
if is_change:
break
for v1, v2, labels in graph.edges_iter(data=True):
if labels["label"] in ordered_contigs:
fout.write("{0} -> {1} [label=\"{2}\", color=\"red\"];\n"
.format(v1, v2, labels["label"]))
elif labels["label"][1:] in all_contigs:
fout.write("{0} -> {1} [label=\"{2}\", color=\"blue\"];\n"
.format(v1, v2, labels["label"]))
else:
fout.write("{0} -> {1};\n".format(v1, v2))
fout.write("}")
fout.close()
def save_colored_overlap_graph(graph_file, scaffolds, out_file):
graph = ar._load_dot(graph_file)
fout = open(out_file, "w")
main_strand = set()
all_contigs = set()
for scf in scaffolds:
for cont in scf.contigs:
main_strand.add(str(cont))
all_contigs.add(cont.name)
fout.write("digraph {\n")
for node in graph.nodes_iter():
if str(node) in main_strand:
fout.write("\"{0}\" [style=filled, fillcolor=red];\n".format(node))
elif str(node)[1:] in all_contigs:
fout.write("\"{0}\" [style=filled, fillcolor=blue];\n".format(node))
for u, v in graph.edges_iter():
fout.write("\"{0}\" -> \"{1}\";\n".format(u, v))
fout.write("}")
fout.close()