def run(self, manager):
manager.logger.info("=" * 80)
manager.logger.info("Assembling with Phylogeny Assembly strategy")
bg = manager.data["gos-asm"]["bg"]
log_bg_stats(bg=bg, logger=manager.logger)
target_multicolor = manager.data["gos-asm"]["target_multicolor"]
assembly_cnt = 0
ap_header_printed = False
kbreaks = []
max_cc_size = 0
for cc_cnt, cc in enumerate(
bg.connected_components_subgraphs(copy=False)):
if len(list(cc.nodes())) > max_cc_size:
max_cc_size = len(list(cc.nodes()))
possible_assemblies_graph = Graph()
for vertex in (v for v in cc.nodes() if v.is_regular_vertex):
if suitable_for_assembly_fragment_ends_vertex(
graph=bg,
reg_vertex=vertex,
target_multicolor=target_multicolor):
possible_assemblies_graph.add_node(vertex)
if len(possible_assemblies_graph.nodes()) > 1:
manager.logger.debug("suitable vertices {}".format(
len(possible_assemblies_graph.nodes())))
# if len(list(possible_assemblies_graph.nodes())) > 1000:
# print("passing large cc")
for v1, v2 in itertools.combinations(
list(possible_assemblies_graph.nodes()), 2):
if assembly_is_allowed(graph=bg, vertex1=v1, vertex2=v2, target_multicolor=target_multicolor, data=manager.data) \
and has_support_edge(graph=bg, v1=v1, v2=v2):
s_edge = bg.get_condensed_edge(vertex1=v1, vertex2=v2)
evolutionary_scenarios = {}
full_ie1_multicolor = get_full_irregular_multicolor(
vertex=v1, data=manager.data, graph=bg)
full_ie2_multicolor = get_full_irregular_multicolor(
vertex=v2, data=manager.data, graph=bg)
for e_scenario_name, e_scenario in non_conflicting_evolutionary_scenarios:
evolutionary_scenarios[
e_scenario_name] = get_assembly_score(
full_ie1_multicolor=full_ie1_multicolor,
full_ie2_multicolor=full_ie2_multicolor,
sedge_multicolor=s_edge.multicolor,
target_multicolor=target_multicolor,
evolutionary_scenario=e_scenario,
data=manager.data)
scenario, maximal_score = get_maximal_phylogenetic_score(
evolutionary_scenarios)
scenario, minimal_score = get_minimal_phylogenetic_score(
evolutionary_scenarios)
if minimal_score > phylo_threshold:
possible_assemblies_graph.add_edge(
v1, v2, attr_dict={"weight": maximal_score})
elif minimal_score == 1:
iedge1 = get_irregular_edge_by_vertex_color(
graph=bg,
vertex=v1,
color=target_multicolor.colors.pop())
iedge2 = get_irregular_edge_by_vertex_color(
graph=bg,
vertex=v2,
color=target_multicolor.colors.pop())
s_edge = bg.get_condensed_edge(vertex1=v1, vertex2=v2)
r1_name, r1_dir = get_repeat_info(iedge1)
r2_name, r2_dir = get_repeat_info(iedge2)
r1_entry = get_repeat_entry(repeat_name=r1_name,
repeat_direction=r1_dir)
r2_entry = get_repeat_entry(repeat_name=r2_name,
repeat_direction=r2_dir)
repeat_info = {
"repeat_name_1": r1_name,
"repeat_name_2": r2_name,
"repeat_dir_1": r1_dir,
"repeat_dir_2": r2_dir
}
try:
repeat_guidance = get_repeat_guidance(
genome=target_multicolor.colors.pop(),
repeat1_entry=r1_entry,
repeat2_entry=r2_entry,
data=manager.data)
except nx.networkx.exception.NetworkXNoPath:
raise Exception(
"Pair of edges must suitable for assembly with repeats guidance"
)
repeat_info["repeat_guidance"] = repeat_guidance
evolutionary_scenarios = {}
full_ie1_multicolor = get_full_irregular_multicolor(
vertex=v1, data=manager.data, graph=bg)
full_ie2_multicolor = get_full_irregular_multicolor(
vertex=v2, data=manager.data, graph=bg)
sedge_multicolor = s_edge.multicolor if s_edge is not None else Multicolor(
)
for e_scenario_name, e_scenario in non_conflicting_evolutionary_scenarios:
evolutionary_scenarios[
e_scenario_name] = get_assembly_score(
full_ie1_multicolor=full_ie1_multicolor,
full_ie2_multicolor=full_ie2_multicolor,
sedge_multicolor=sedge_multicolor,
target_multicolor=target_multicolor,
evolutionary_scenario=e_scenario,
data=manager.data)
api = AssemblyPointInfo(
support_edge=s_edge,
iedge1=iedge1,
iedge2=iedge2,
evolutionary_scenarios=evolutionary_scenarios,
allowed=True,
repeat_info=repeat_info,
target_multicolor=target_multicolor,
target_color=target_multicolor)
ap = AssemblyPoint(vertex1=v1,
vertex2=v2,
additional_information=api)
ap.cc_id = cc_cnt
manager.logger.debug(
"Identified TEMP assembly point :: {ap}".format(
ap=ap.as_logger_entry(), ))
matching_graph = nx.max_weight_matching(
G=possible_assemblies_graph)
processed_vertices = set()
for v1, v2 in matching_graph:
if v1 in processed_vertices or v2 in processed_vertices:
continue
processed_vertices.add(v1)
processed_vertices.add(v2)
for color in target_multicolor.colors:
iedge1 = get_irregular_edge_by_vertex_color(graph=bg,
vertex=v1,
color=color)
iedge2 = get_irregular_edge_by_vertex_color(graph=bg,
vertex=v2,
color=color)
s_edge = bg.get_condensed_edge(vertex1=v1, vertex2=v2)
r1_name, r1_dir = get_repeat_info(iedge1)
r2_name, r2_dir = get_repeat_info(iedge2)
r1_entry = get_repeat_entry(repeat_name=r1_name,
repeat_direction=r1_dir)
r2_entry = get_repeat_entry(repeat_name=r2_name,
repeat_direction=r2_dir)
repeat_info = {
"repeat_name_1": r1_name,
"repeat_name_2": r2_name,
"repeat_dir_1": r1_dir,
"repeat_dir_2": r2_dir
}
try:
repeat_guidance = get_repeat_guidance(
genome=color,
repeat1_entry=r1_entry,
repeat2_entry=r2_entry,
data=manager.data)
except nx.networkx.exception.NetworkXNoPath:
raise Exception(
"Pair of edges must suitable for assembly with repeats guidance"
)
repeat_info["repeat_guidance"] = repeat_guidance
evolutionary_scenarios = {}
full_ie1_multicolor = get_full_irregular_multicolor(
vertex=v1, data=manager.data, graph=bg)
full_ie2_multicolor = get_full_irregular_multicolor(
vertex=v2, data=manager.data, graph=bg)
sedge_multicolor = s_edge.multicolor if s_edge is not None else Multicolor(
)
for e_scenario_name, e_scenario in non_conflicting_evolutionary_scenarios:
evolutionary_scenarios[
e_scenario_name] = get_assembly_score(
full_ie1_multicolor=full_ie1_multicolor,
full_ie2_multicolor=full_ie2_multicolor,
sedge_multicolor=sedge_multicolor,
target_multicolor=target_multicolor,
evolutionary_scenario=e_scenario,
data=manager.data)
api = AssemblyPointInfo(
support_edge=s_edge,
iedge1=iedge1,
iedge2=iedge2,
evolutionary_scenarios=evolutionary_scenarios,
allowed=True,
repeat_info=repeat_info,
target_multicolor=target_multicolor,
target_color=Multicolor(color))
ap = AssemblyPoint(vertex1=v1,
vertex2=v2,
additional_information=api)
ap.cc_id = cc_cnt
if not ap_header_printed:
ap_header_printed = True
manager.logger.debug(
"-" * 32 + "-" *
len(AssemblyPoint.logger_file_header_string()))
manager.logger.debug(
" " * 32 +
AssemblyPoint.logger_file_header_string())
manager.logger.debug(
"-" * 32 + "-" *
len(AssemblyPoint.logger_file_header_string()))
manager.logger.debug(
"Identified an assembly point :: {ap}".format(
ap=ap.as_logger_entry()))
manager.data["gos-asm"]["assembly_points"].append(ap)
k_break = create_k_break_from_assembly_point(
assembly_point=ap)
kbreaks.append(k_break)
# print(max_cc_size)
manager.logger.debug("-" * 32 + "-" *
len(AssemblyPoint.logger_file_header_string()))
for k_break in kbreaks:
bg.apply_kbreak(kbreak=k_break, merge=False)
assembly_cnt += 1
manager.logger.info(
"Identified and performed {gluing_cnt} assemblies with Phylogeny Assembly strategy"
"".format(gluing_cnt=assembly_cnt))
log_bg_stats(bg=bg, logger=manager.logger)
def run(self, manager):
manager.logger.info("=" * 80)
manager.logger.info("Assembling with Connected Components Assembly Strategy Using MGRA guidance graph")
manager.logger.info("Strategy version 2")
bg = manager.data["gos-asm"]["bg"]
guidance_graph = manager.data["mgra"]["guidance_graph"]
guidance_graph = get_balance_graph(breakpoint_graph=guidance_graph)
log_bg_stats(bg=bg, logger=manager.logger)
log_bg_stats(bg=guidance_graph, logger=manager.logger)
target_multicolor = manager.data["gos-asm"]["target_multicolor"]
assembly_cnt = 0
ap_header_printed = False
kbreaks = []
for cc_cnt, cc in enumerate(guidance_graph.connected_components_subgraphs(copy=False)):
possible_assemblies_graph = Graph()
for vertex in (v for v in cc.nodes() if v.is_regular_vertex):
if suitable_for_assembly_fragment_ends_vertex(graph=bg, reg_vertex=vertex, target_multicolor=target_multicolor):
possible_assemblies_graph.add_node(vertex)
if len(list(possible_assemblies_graph.nodes())) > 1000:
continue
for v1, v2 in itertools.combinations(list(possible_assemblies_graph.nodes()), 2):
if assembly_is_allowed(graph=bg, vertex1=v1, vertex2=v2, target_multicolor=target_multicolor, data=manager.data):
possible_assemblies_graph.add_edge(v1, v2)
reg_vertices_for_assembly = set()
for pag_cc in nx.connected_component_subgraphs(possible_assemblies_graph, copy=False):
if len(list(pag_cc.nodes())) != 2:
continue
reg_vertices_for_assembly.add(tuple(pag_cc.nodes()))
for vertex_pair in reg_vertices_for_assembly:
v1, v2 = vertex_pair
if v1.block_name == v2.block_name:
continue
for color in target_multicolor.colors:
iedge1 = get_irregular_edge_by_vertex_color(graph=bg, vertex=v1, color=color)
iedge2 = get_irregular_edge_by_vertex_color(graph=bg, vertex=v2, color=color)
fr1_name = get_from_dict_with_path(iedge1.data, key="name", path=["fragment"])
fr2_name = get_from_dict_with_path(iedge2.data, key='name', path=["fragment"])
if fr1_name == fr2_name:
continue
s_edge = bg.get_condensed_edge(vertex1=v1, vertex2=v2) if bg.has_edge(vertex1=v1, vertex2=v2) else None
r1_name, r1_dir = get_repeat_info(iedge1)
r2_name, r2_dir = get_repeat_info(iedge2)
r1_entry = get_repeat_entry(repeat_name=r1_name, repeat_direction=r1_dir)
r2_entry = get_repeat_entry(repeat_name=r2_name, repeat_direction=r2_dir)
repeat_info = {
"repeat_name_1": r1_name,
"repeat_name_2": r2_name,
"repeat_dir_1": r1_dir,
"repeat_dir_2": r2_dir
}
try:
repeat_guidance = get_repeat_guidance(genome=color, repeat1_entry=r1_entry, repeat2_entry=r2_entry, data=manager.data)
except nx.networkx.exception.NetworkXNoPath:
raise Exception("Pair of edges must suitable for assembly with repeats guidance")
repeat_info["repeat_guidance"] = repeat_guidance
evolutionary_scenarios = {}
full_ie1_multicolor = get_full_irregular_multicolor(vertex=v1, data=manager.data, graph=bg)
full_ie2_multicolor = get_full_irregular_multicolor(vertex=v2, data=manager.data, graph=bg)
sedge_multicolor = s_edge.multicolor if s_edge is not None else Multicolor()
for e_scenario_name, e_scenario in non_conflicting_evolutionary_scenarios:
evolutionary_scenarios[e_scenario_name] = get_assembly_score(full_ie1_multicolor=full_ie1_multicolor,
full_ie2_multicolor=full_ie2_multicolor,
sedge_multicolor=sedge_multicolor,
target_multicolor=target_multicolor,
evolutionary_scenario=e_scenario, data=manager.data)
api = AssemblyPointInfo(support_edge=s_edge, iedge1=iedge1, iedge2=iedge2,
evolutionary_scenarios=evolutionary_scenarios,
allowed=True, repeat_info=repeat_info, target_multicolor=target_multicolor,
target_color=Multicolor(color))
ap = AssemblyPoint(vertex1=v1, vertex2=v2, additional_information=api)
ap.cc_id = cc_cnt
if not ap_header_printed:
ap_header_printed = True
manager.logger.debug("-"*32 + "-"*len(AssemblyPoint.logger_file_header_string()))
manager.logger.debug(" "*32 + AssemblyPoint.logger_file_header_string())
manager.logger.debug("-"*32 + "-"*len(AssemblyPoint.logger_file_header_string()))
manager.logger.debug("Identified an assembly point :: {ap}".format(ap=ap.as_logger_entry()))
manager.data["gos-asm"]["assembly_points"].append(ap)
k_break = create_k_break_from_assembly_point(assembly_point=ap)
kbreaks.append(k_break)
manager.logger.debug("-"*32 + "-"*len(AssemblyPoint.logger_file_header_string()))
for k_break in kbreaks:
bg.apply_kbreak(kbreak=k_break, merge=False)
assembly_cnt += 1
manager.logger.info("Identified and performed {gluing_cnt} assemblies with Connected Components Assembly strategy"
"".format(gluing_cnt=assembly_cnt))
log_bg_stats(bg=bg, logger=manager.logger)