def run(self, manager):
manager.logger.info("Reading blocks orders data")
file_paths = manager.configuration["gos-asm"]["input"]["block_orders_file_paths"]
bg = BreakpointGraph()
for file_path in file_paths:
with open(file_path, "rt") as source:
bg.update(breakpoint_graph=GRIMMReader.get_breakpoint_graph(stream=source, merge_edges=False), merge_edges=False)
manager.data["gos-asm"]["bg"] = bg
manager.logger.info("Reading phylogenetic tree information")
tree = NewickReader.from_string(data_string=manager.configuration["gos-asm"]["input"]["phylogenetic_tree"])
manager.data["gos-asm"]["phylogenetic_tree"] = tree
full_tmc = Multicolor(*[BGGenome(genome_name) for genome_name in manager.configuration["gos-asm"]["input"]["target_organisms"]])
manager.data["gos-asm"]["target_multicolor"] = full_tmc
tree_consistent_target_multicolors = Multicolor.split_colors(full_tmc,
guidance=tree.consistent_multicolors,
account_for_color_multiplicity_in_guidance=False)
for target_multicolor in tree_consistent_target_multicolors[:]:
for tree_c_multicolor in deepcopy(tree.consistent_multicolors):
if tree_c_multicolor <= target_multicolor \
and tree_c_multicolor not in tree_consistent_target_multicolors \
and len(tree_c_multicolor.colors) > 0:
tree_consistent_target_multicolors.append(tree_c_multicolor)
tree_consistent_target_multicolors = sorted(tree_consistent_target_multicolors,
key=lambda mc: len(mc.hashable_representation),
reverse=True)
all_target_multicolors = tree_consistent_target_multicolors[:]
for i in range(2, len(tree_consistent_target_multicolors) + 1):
for comb in itertools.combinations(tree_consistent_target_multicolors[:], i):
comb = list(comb)
for mc1, mc2 in itertools.combinations(comb, 2):
if len(mc1.intersect(mc2).colors) > 0:
break
else:
new_mc = Multicolor()
for mc in comb:
new_mc += mc
all_target_multicolors.append(new_mc)
hashed_vertex_tree_consistent_multicolors = {mc.hashable_representation for mc in all_target_multicolors}
all_target_multicolors = [Multicolor(*hashed_multicolor) for hashed_multicolor in
hashed_vertex_tree_consistent_multicolors]
all_target_multicolors = sorted(all_target_multicolors,
key=lambda mc: len(mc.hashable_representation),
reverse=True)
manager.data["gos-asm"]["target_multicolors"] = all_target_multicolors
# log_bg_stats(bg=bg, logger=manager.logger)
manager.logger.info("Reading repeats-bridges information")
manager.data["gos-asm"]["repeats_guidance"] = get_repeats_bridges_guidance(
file_name=manager.configuration["gos-asm"]["input"]["repeats_bridges_file"], data=manager.data)
def validate_datasets(root_directory):
root_directory = path.abspath(root_directory)
for root, dirs, files in walk(root_directory):
for f in files:
block_file_path = path.join(root, f)
_, e1, e2 = map(int, path.basename(path.dirname(path.dirname(block_file_path))).split('_'))
with open(block_file_path) as block_file:
breakpoint_graph = GRIMMReader.get_breakpoint_graph(block_file)
for genomes in PAIRS_TO_CHECK:
leaf_distance = get_dcj_distance_two_genomes(breakpoint_graph, genomes)
if leaf_distance != e2:
print('Leaf - inner node distance differs in file {0}, expected={1}, real={2}'.
format(block_file_path, e2, leaf_distance))
inner_node_distance = get_dcj_distance_two_genomes(breakpoint_graph, ('Left', 'Right'))
if inner_node_distance != e1:
print('Inner node distance differs in file {0}, expected={1}, real={2}'.
format(block_file_path, e1, inner_node_distance))
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_metrics_on_block_file(block_path, full_correct_tree_file_name):
correct_tree = read_correct_tree(full_correct_tree_file_name)
with open(block_path) as block_file:
breakpoint_graph = GRIMMReader.get_breakpoint_graph(block_file)
return compare_metric_results(breakpoint_graph, correct_tree)
