https://github.com/fenderglass/Ragout
Tip revision: 4b42ddec7d839ab6369faa31a49e2d3a8db7d124 authored by fenderglass on 26 April 2014, 05:29:56 UTC
instal
instal
Tip revision: 4b42dde
main.py
#!/usr/bin/env python
##################################
#The main Ragout module
##################################
import os
import sys
import logging
import argparse
import overlap.overlap as ovlp
import assembly_graph.assembly_refine as asref
import breakpoint_graph.breakpoint_graph as bg
from breakpoint_graph.phylogeny import Phylogeny
from breakpoint_graph.permutation import PermutationContainer
import scaffolder.scaffolder as scfldr
import scaffolder.merge_iters as merge
from synteny_backend.synteny_backend import SyntenyBackend
import parsers.config_parser as cparser
from shared.debug import DebugConfig
#register backends
import synteny_backend.sibelia
import synteny_backend.cactus
logger = logging.getLogger()
debugger = DebugConfig.get_instance()
def enable_logging(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.setLevel(logging.INFO)
console_log.setFormatter(console_formatter)
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)
#top-level logic of program
def do_job(config_file, out_dir, backend, assembly_refine,
circular_refs, overwrite, debug):
if not os.path.isdir(out_dir):
os.mkdir(out_dir)
if debug:
core_debug = os.path.join(out_dir, "debug")
debugger.set_debug_dir(core_debug)
config = cparser.parse_ragout_config(config_file)
phylogeny = Phylogeny(config.tree)
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")
enable_logging(out_log)
logger.info("Cooking Ragout...")
backends = SyntenyBackend.get_available_backends()
if not backends[backend].make_permutations(config, out_dir, overwrite):
logger.error("There were problems with synteny backend, exiting.")
return
last_scaffolds = None
for block_size in config.blocks:
logger.info("Running Ragout with the block size {0}".format(block_size))
block_dir = os.path.join(out_dir, str(block_size))
block_config = os.path.join(block_dir, "blocks.cfg")
block_order = os.path.join(block_dir, "scaffolds.ord")
if debug:
debug_dir = os.path.join(core_debug, str(block_size))
debugger.set_debug_dir(debug_dir)
perm_container = PermutationContainer(block_config)
graph = bg.BreakpointGraph()
graph.build_from(perm_container, circular_refs)
connections = graph.find_adjacencies(phylogeny)
scaffolds = scfldr.get_scaffolds(connections, perm_container)
scfldr.output_order(scaffolds, block_order)
if last_scaffolds:
last_scaffolds = merge.merge(last_scaffolds, scaffolds)
else:
last_scaffolds = scaffolds
scfldr.output_order(last_scaffolds, out_order)
scfldr.output_fasta(config.targets, last_scaffolds, out_scaffolds)
if assembly_refine:
if not ovlp.make_overlap_graph(config.targets, out_overlap):
logger.error("Error in overlap graph reconstruction, exiting")
return
refined_scaffolds = asref.refine_scaffolds(out_overlap, last_scaffolds)
scfldr.output_order(refined_scaffolds, out_refined_order)
scfldr.output_fasta(config.targets, refined_scaffolds,
out_refined_scaffolds)
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("config", metavar="config_file",
help="path to the configuration 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",
help="which tool to use for synteny block decomposition.",
choices=["sibelia", "cactus"])
parser.add_argument("--refine", action="store_const", metavar="assembly_refine",
dest="assembly_refine", default=False, const=True,
help="refine with the assembly graph")
parser.add_argument("--circular", action="store_const",
dest="circular_refs", default=False, const=True,
help="treat input references as circular")
parser.add_argument("--overwrite", action="store_const",
dest="overwrite", default=False, const=True,
help="overwrite existing Sibelia/Cactus results")
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."
"Use \"scripts/install-deps.py\" to install it.\n")
return
do_job(args.config, args.output_dir, args.synteny_backend,
args.assembly_refine, args.circular_refs, args.overwrite, args.debug)
if __name__ == "__main__":
main()