def __init__(self,
maf,
ancestor,
ancestor_fasta,
phylo,
outDir="ragout_out",
scale="large",
outLog="ragout_log",
is_overwrite=True,
is_debug=True,
is_resolve_repeats=False,
is_solid_scaffolds=False):
self.maf = maf
self.ancestor = ancestor
self.ancestor_seqs = read_fasta_dict(ancestor_fasta)
self.scale = scale
self.debug = is_debug
self.outDir = "_".join([outDir, ancestor])
self.backend = SyntenyBackend.backends["maf"]
self.overwrite = is_overwrite
self.logger = enable_logging("_".join([outLog, ancestor]), is_debug)
self.debugger = DebugConfig.get_instance()
self.is_solid_scaffolds = is_solid_scaffolds
self.is_resolve_repeats = is_resolve_repeats
self.synteny_blocks = config.vals["blocks"][self.scale]
if not os.path.isdir(self.outDir):
os.mkdir(self.outDir)
self._set_debugging()
self._check_extern_modules()
self._get_phylogeny_and_naming_ref(phylo)
self._make_recipe(phylo)
self._make_permutaion_files()
self._make_run_stages()
self._make_stage_perms()
pass
"""
This module infers missing adjacencies
by recovering perfect matching
"""
from collections import namedtuple
import logging
import os
from copy import copy
import networkx as nx
from ragout.shared.debug import DebugConfig
logger = logging.getLogger()
debugger = DebugConfig.get_instance()
Adjacency = namedtuple("Adjacency", ["block", "distance",
"supporting_genomes", "infinity"])
class AdjacencyInferer(object):
def __init__(self, breakpoint_graph, phylogeny, ancestral = False):
self.main_graph = breakpoint_graph
self.phylogeny = phylogeny
self.ancestral = ancestral
def infer_adjacencies(self, debug=False, filename="adjacencies.txt"):
"""
Infers missing adjacencies by recovering perfect matching
"""
logger.info("Inferring missing adjacencies")