#(c) 2013-2014 by Authors #This file is a part of Ragout program. #Released under the BSD license (see LICENSE file) """ The main Ragout module. It defines top-level logic of the program """ import os import sys import shutil import logging import argparse import ragout.overlap.overlap as ovlp import ragout.assembly_graph.assembly_refine as asref import ragout.assembly_graph.assembly_graph as asgraph import ragout.breakpoint_graph.breakpoint_graph as bg import ragout.scaffolder.scaffolder as scfldr import ragout.scaffolder.merge_iters as merge import ragout.overlap.overlap as overlap import ragout.maf2synteny.maf2synteny as m2s from ragout.breakpoint_graph.phylogeny import Phylogeny, PhyloException from ragout.breakpoint_graph.permutation import (PermutationContainer, PermException) from ragout.synteny_backend.synteny_backend import SyntenyBackend from ragout.parsers.recipe_parser import parse_ragout_recipe, RecipeException from ragout.parsers.fasta_parser import read_fasta_dict, FastaError from ragout.shared.debug import DebugConfig #register backends import synteny_backend.sibelia import synteny_backend.cactus import synteny_backend.maf logger = logging.getLogger() debugger = DebugConfig.get_instance() def enable_logging(log_file, debug): """ Turns on logging, sets debug levels and assigns a log file """ log_formatter = logging.Formatter("[%(asctime)s] %(name)s: %(levelname)s: " "%(message)s", "%H:%M:%S") console_formatter = logging.Formatter("[%(asctime)s] %(levelname)s: " "%(message)s", "%H:%M:%S") console_log = logging.StreamHandler() console_log.setFormatter(console_formatter) if not debug: console_log.setLevel(logging.INFO) file_handler = logging.FileHandler(log_file, mode="w") file_handler.setFormatter(log_formatter) logger.setLevel(logging.DEBUG) logger.addHandler(console_log) logger.addHandler(file_handler) def check_extern_modules(backend): """ Checks if all neccessary native modules are available """ backends = SyntenyBackend.get_available_backends() if backend not in backends: logger.error("\"{0}\" is not installed. You can use provided scripts " "to install it".format(backend)) return False if not m2s.check_binary(): return False if not overlap.check_binary(): return False return True def do_job(recipe_file, out_dir, backend, assembly_refine, overwrite, debug): """ Top-level logic of program """ out_log = os.path.join(out_dir, "ragout.log") out_order = os.path.join(out_dir, "scaffolds.ord") out_scaffolds = os.path.join(out_dir, "scaffolds.fasta") out_overlap = os.path.join(out_dir, "contigs_overlap.dot") out_refined_order = os.path.join(out_dir, "scaffolds_refined.ord") out_refined_scaffolds = os.path.join(out_dir, "scaffolds_refined.fasta") debug_root = os.path.join(out_dir, "debug") if not os.path.isdir(out_dir): os.mkdir(out_dir) if debug: debugger.set_debug_dir(debug_root) debugger.clear_debug_dir() enable_logging(out_log, debug) logger.info("Cooking Ragout...") if not check_extern_modules(backend): return 1 try: recipe = parse_ragout_recipe(recipe_file) target_fasta_file = recipe["genomes"][recipe["target"]]["fasta"] target_fasta_dict = read_fasta_dict(target_fasta_file) phylogeny = Phylogeny(recipe) except (RecipeException, FastaError, PhyloException) as e: logger.error(e) return 1 backends = SyntenyBackend.get_available_backends() perm_files = backends[backend].make_permutations(recipe, out_dir, overwrite) if not perm_files: logger.error("There were problems with synteny backend, exiting.") return 1 last_scaffolds = None for block_size in recipe["blocks"]: logger.info("Running Ragout with the block size {0}".format(block_size)) if debug: debug_dir = os.path.join(debug_root, str(block_size)) debugger.set_debug_dir(debug_dir) try: perm_container = PermutationContainer(perm_files[block_size], recipe) except PermException as e: logger.error(e) return 1 graph = bg.BreakpointGraph() graph.build_from(perm_container, recipe) adjacencies = graph.find_adjacencies(phylogeny) scaffolds = scfldr.get_scaffolds(adjacencies, perm_container) if last_scaffolds: last_scaffolds = merge.merge(last_scaffolds, scaffolds) else: last_scaffolds = scaffolds debugger.set_debug_dir(debug_root) scfldr.output_order(last_scaffolds, out_order) scfldr.output_fasta(target_fasta_dict, last_scaffolds, out_scaffolds) if assembly_refine: if not ovlp.make_overlap_graph(target_fasta_file, out_overlap): logger.error("Error in overlap graph reconstruction, exiting") return 1 refined_scaffolds = asref.refine_scaffolds(out_overlap, last_scaffolds, target_fasta_dict) scfldr.output_order(refined_scaffolds, out_refined_order) scfldr.output_fasta(target_fasta_dict, refined_scaffolds, out_refined_scaffolds) if debug: shutil.copy(out_overlap, debugger.debug_dir) out_colored_overlap = os.path.join(debugger.debug_dir, "colored_overlap.dot") asgraph.save_colored_insert_overlap_graph(out_overlap, last_scaffolds, refined_scaffolds, out_colored_overlap) os.remove(out_overlap) logger.info("Your Ragout is ready!") def main(): parser = argparse.ArgumentParser(description="A tool for assisted assembly" " using multiple references", formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument("recipe", metavar="recipe_file", help="path to recipe file") parser.add_argument("-o", "--outdir", dest="output_dir", help="path to the working directory", default="ragout-out") parser.add_argument("-s", "--synteny", dest="synteny_backend", default="sibelia", choices=["sibelia", "cactus", "maf"], help="which tool to use for synteny block decomposition") parser.add_argument("--refine", action="store_const", metavar="assembly_refine", dest="assembly_refine", default=False, const=True, help="enable refinement with assembly graph") parser.add_argument("--overwrite", action="store_const", dest="overwrite", default=False, const=True, help="overwrite existing synteny blocks") parser.add_argument("--debug", action="store_const", dest="debug", default=False, const=True, help="enable debug output") parser.add_argument("--version", action="version", version="Ragout v0.3b") args = parser.parse_args() return do_job(args.recipe, args.output_dir, args.synteny_backend, args.assembly_refine, args.overwrite, args.debug)