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 v0.2b")
args = parser.parse_args()
backends = SyntenyBackend.get_available_backends()
if args.synteny_backend not in backends:
sys.stderr.write(args.synteny_backend + " is not installed. "
"You can use provided scripts to install it.\n")
return 1
return do_job(args.recipe, args.output_dir, args.synteny_backend,
args.assembly_refine, args.overwrite, args.debug)
def do_job(recipe_file, out_dir, backend, assembly_refine,
overwrite, debug):
if not os.path.isdir(out_dir):
os.mkdir(out_dir)
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_colored_overlap = os.path.join(out_dir, "colored_contigs_overlap.dot")
out_compress_overlap = os.path.join(out_dir, "compress_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")
if debug:
core_debug = os.path.join(out_dir, "debug")
debugger.set_debug_dir(core_debug)
enable_logging(out_log, debug)
logger.info("Cooking Ragout...")
backends = SyntenyBackend.get_available_backends()
try:
recipe = parse_ragout_recipe(recipe_file)
except RecipeException as e:
logger.error("Error parsing recipe")
logger.error(e)
return 1
try:
phylogeny = Phylogeny(recipe)
except PhyloException as e:
logger.error(e)
return 1
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(core_debug, 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)
connections = graph.find_adjacencies(phylogeny)
scaffolds = scfldr.get_scaffolds(connections, perm_container)
if debug:
ord_path = os.path.join(debug_dir, "scaffolds.ord")
scfldr.output_order(scaffolds, ord_path)
if last_scaffolds:
last_scaffolds = merge.merge(last_scaffolds, scaffolds)
else:
last_scaffolds = scaffolds
target_fasta = recipe["genomes"][recipe["target"]]["fasta"]
scfldr.output_order(last_scaffolds, out_order)
scfldr.output_fasta(target_fasta, last_scaffolds, out_scaffolds)
if assembly_refine:
if not ovlp.make_overlap_graph(target_fasta, out_overlap):
logger.error("Error in overlap graph reconstruction, exiting")
return 1
refined_scaffolds = asref.refine_scaffolds(out_overlap, last_scaffolds)
#asgraph.save_colored_insert_overlap_graph(out_overlap, last_scaffolds,
# refined_scaffolds,
# out_colored_overlap)
scfldr.output_order(refined_scaffolds, out_refined_order)
scfldr.output_fasta(target_fasta, refined_scaffolds,
out_refined_scaffolds)
logger.info("Your Ragout is ready!")