def __init__(self,
vertex1=None,
vertex2=None,
fragment1=None,
fragment2=None,
sign1=None,
sign2=None,
additional_information=None,
cc_id=None):
self.vertex1 = vertex1
self.vertex2 = vertex2
self.target_multicolor = None if additional_information is None else additional_information.target_multicolor
self.info = additional_information
self.fragment1 = None if additional_information is None else get_from_dict_with_path(
additional_information.iedge1.data, key="name", path=["fragment"])
self.fragment2 = None if additional_information is None else get_from_dict_with_path(
additional_information.iedge2.data, key="name", path=["fragment"])
fr1_fo = None if additional_information is None else get_from_dict_with_path(
additional_information.iedge1.data,
key="forward_orientation",
path=["fragment"])
self.fragment1_sign = None if fr1_fo is None else (
"+" if vertex1 == fr1_fo[0] else "-")
fr2_fo = None if additional_information is None else get_from_dict_with_path(
additional_information.iedge2.data,
key="forward_orientation",
path=["fragment"])
self.fragment2_sign = None if fr2_fo is None else (
"+" if vertex2 == fr2_fo[1] else "-")
self.id = AssemblyPoint.id_cnt
self.cc_id = cc_id
AssemblyPoint.id_cnt += 1
def run(self, manager):
mgra_ex_path = get_from_dict_with_path(manager.configuration,
key="executable_path",
path=["mgra"])
manager.logger.info("=" * 80)
if mgra_ex_path is None:
manager.logger.info(
"MGRA executable path is not supplied, skipping the MGRA based tasks"
)
return
manager.logger.info(
"Preparing data to communicate with MGRA and ontain guidance graph"
)
temp_dir = os.path.join(
manager.configuration["gos-asm"]["output"]["dir"], "tmp_mgra")
if not os.path.exists(temp_dir):
os.mkdir(temp_dir)
blocks_file_name = os.path.join(temp_dir, "blocks.txt")
config_file_name = os.path.join(temp_dir, "config.cfg")
mgra_output_dir_name = os.path.join(temp_dir, "output/")
manager.logger.debug(
"Writing blocks orders in GRIMM format to {file_name}".format(
file_name=blocks_file_name))
GRIMMWriter.print_genomes_as_grimm_blocks_orders(
bg=manager.data["gos-asm"]["bg"], file_name=blocks_file_name)
manager.logger.debug(
"Writing configuration file for MGRA run to {file_name}".format(
file_name=config_file_name))
config = self.create_mgra_config(blocks_file_name=blocks_file_name,
manager=manager)
with open(config_file_name, "wt") as destination:
json.dump(obj=config, fp=destination)
manager.logger.info("Running MGRA on prepared configuration")
os.system("{mgra_ex_path} -c {config_file_path} -o {output_dir_path}"
"".format(mgra_ex_path=mgra_ex_path,
config_file_path=config_file_name,
output_dir_path=mgra_output_dir_name))
manager.logger.debug("MGRA has successfully finished")
manager.logger.info("Reading MGRA produced guidance graph")
genomes_dir = os.path.join(mgra_output_dir_name, "genomes")
genome_files = [
name for name in os.listdir(genomes_dir) if name.endswith(".gen")
]
full_genomes_paths = [
os.path.join(genomes_dir, name) for name in genome_files
]
guidance_bg = BreakpointGraph()
for file_name in full_genomes_paths:
with open(file_name, "rt") as source:
guidance_bg.update(
breakpoint_graph=GRIMMReader.get_breakpoint_graph(
stream=source, merge_edges=False),
merge_edges=False)
if "mgra" not in manager.data:
manager.data["mgra"] = {}
manager.data["mgra"]["guidance_graph"] = guidance_bg
manager.logger.info("Obtained MGRA produced guidance graph")
def __init__(self, vertex1=None, vertex2=None,
fragment1=None, fragment2=None,
sign1=None, sign2=None,
additional_information=None, cc_id=None):
self.vertex1 = vertex1
self.vertex2 = vertex2
self.target_multicolor = None if additional_information is None else additional_information.target_multicolor
self.info = additional_information
self.fragment1 = None if additional_information is None else get_from_dict_with_path(additional_information.iedge1.data, key="name",
path=["fragment"])
self.fragment2 = None if additional_information is None else get_from_dict_with_path(additional_information.iedge2.data, key="name",
path=["fragment"])
fr1_fo = None if additional_information is None else get_from_dict_with_path(additional_information.iedge1.data,
key="forward_orientation", path=["fragment"])
self.fragment1_sign = None if fr1_fo is None else ("+" if vertex1 == fr1_fo[0] else "-")
fr2_fo = None if additional_information is None else get_from_dict_with_path(additional_information.iedge2.data,
key="forward_orientation", path=["fragment"])
self.fragment2_sign = None if fr2_fo is None else ("+" if vertex2 == fr2_fo[1] else "-")
self.id = AssemblyPoint.id_cnt
self.cc_id = cc_id
AssemblyPoint.id_cnt += 1
def run(self, manager):
mgra_ex_path = get_from_dict_with_path(manager.configuration, key="executable_path", path=["mgra"])
manager.logger.info("=" * 80)
if mgra_ex_path is None:
manager.logger.info("MGRA executable path is not supplied, skipping the MGRA based tasks")
return
manager.logger.info("Preparing data to communicate with MGRA and ontain guidance graph")
temp_dir = os.path.join(manager.configuration["gos-asm"]["output"]["dir"], "tmp_mgra")
if not os.path.exists(temp_dir):
os.mkdir(temp_dir)
blocks_file_name = os.path.join(temp_dir, "blocks.txt")
config_file_name = os.path.join(temp_dir, "config.cfg")
mgra_output_dir_name = os.path.join(temp_dir, "output/")
manager.logger.debug("Writing blocks orders in GRIMM format to {file_name}".format(file_name=blocks_file_name))
GRIMMWriter.print_genomes_as_grimm_blocks_orders(bg=manager.data["gos-asm"]["bg"],
file_name=blocks_file_name)
manager.logger.debug("Writing configuration file for MGRA run to {file_name}".format(file_name=config_file_name))
config = self.create_mgra_config(blocks_file_name=blocks_file_name, manager=manager)
with open(config_file_name, "wt") as destination:
json.dump(obj=config, fp=destination)
manager.logger.info("Running MGRA on prepared configuration")
os.system("{mgra_ex_path} -c {config_file_path} -o {output_dir_path}"
"".format(mgra_ex_path=mgra_ex_path,
config_file_path=config_file_name,
output_dir_path=mgra_output_dir_name))
manager.logger.debug("MGRA has successfully finished")
manager.logger.info("Reading MGRA produced guidance graph")
genomes_dir = os.path.join(mgra_output_dir_name, "genomes")
genome_files = [name for name in os.listdir(genomes_dir) if name.endswith(".gen")]
full_genomes_paths = [os.path.join(genomes_dir, name) for name in genome_files]
guidance_bg = BreakpointGraph()
for file_name in full_genomes_paths:
with open(file_name, "rt") as source:
guidance_bg.update(breakpoint_graph=GRIMMReader.get_breakpoint_graph(stream=source, merge_edges=False), merge_edges=False)
if "mgra" not in manager.data:
manager.data["mgra"] = {}
manager.data["mgra"]["guidance_graph"] = guidance_bg
manager.logger.info("Obtained MGRA produced guidance graph")
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)
