get_organelle_from_assembly.py

#!/usr/bin/env python


try:
    from math import inf
except ImportError:
    inf = float("inf")
from argparse import ArgumentParser
import GetOrganelleLib
from GetOrganelleLib.pipe_control_func import *
from GetOrganelleLib.seq_parser import read_fasta, detect_plastome_architecture, DEGENERATE_BASES
import time
import random
import subprocess
import sys
import os
from copy import deepcopy
from shutil import copyfile, rmtree
PATH_OF_THIS_SCRIPT = os.path.split(os.path.realpath(__file__))[0]
import platform

SYSTEM_NAME = ""
if platform.system() == "Linux":
    SYSTEM_NAME = "linux"
elif platform.system() == "Darwin":
    SYSTEM_NAME = "macOS"
else:
    sys.stdout.write("Error: currently GetOrganelle is not supported for " + platform.system() + "! ")
    exit()
GO_LIB_PATH = os.path.split(GetOrganelleLib.__file__)[0]
GO_DEP_PATH = os.path.realpath(os.path.join(GO_LIB_PATH, "..", "GetOrganelleDep", SYSTEM_NAME))
UTILITY_PATH = os.path.join(PATH_OF_THIS_SCRIPT, "Utilities")

_GO_PATH = GO_PATH
_LBL_DB_PATH = LBL_DB_PATH
_SEQ_DB_PATH = SEQ_DB_PATH

MAJOR_VERSION, MINOR_VERSION = sys.version_info[:2]
if MAJOR_VERSION == 2 and MINOR_VERSION >= 7:
    PYTHON_VERSION = "2.7+"
elif MAJOR_VERSION == 3 and MINOR_VERSION >= 5:
    PYTHON_VERSION = "3.5+"
else:
    sys.stdout.write("Python version have to be 2.7+ or 3.5+")
    sys.exit(0)


def get_options(description, version):
    usage = str(os.path.basename(__file__) + " -g assembly_graph_file -F embplant_pt -o output --min-depth 10")
    parser = ArgumentParser(usage=usage, description=description, add_help=False)
    if "-h" in sys.argv:
        parser.add_argument("-F", dest="organelle_type",
                            help="Target organelle genome type(s): "
                                 "embplant_pt/other_pt/embplant_mt/embplant_nr/animal_mt/fungus_mt/fungus_nr/anonym/"
                                 "embplant_pt,embplant_mt/other_pt,embplant_mt,fungus_mt")
        parser.add_argument("-g", dest="input_graph", help="Input assembly graph (fastg/gfa) file.")
        parser.add_argument("-o", dest="output_base", help="Output directory.")
        parser.add_argument("--min-depth", dest="min_depth", default=0., type=float,
                            help="Minimum depth threshold of contigs. Default: %(default)s.")
        parser.add_argument("--max-depth", dest="max_depth", default=inf, type=float,
                            help="Maximum depth threshold of contigs. Default: %(default)s.")
        parser.add_argument("--no-slim", dest="no_slim",
                            help="Disable the slimming process and directly disentangle the assembly graph.")
        parser.add_argument("-t", dest="threads", type=int, default=1,
                            help="Maximum threads to use. Default: %(default)s.")
        parser.add_argument("--continue", dest="script_resume", default=False, action="store_true",
                            help="Resume a previous run. Default: %(default)s.")
        parser.print_help()
        sys.stdout.write("\n")
        exit()
    else:
        parser.add_argument("-F", dest="organelle_type",
                            help="This flag should be followed with embplant_pt (embryophyta plant plastome), "
                                 "other_pt (non-embryophyta plant plastome), embplant_mt "
                                 "(plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt "
                                 "(animal mitochondrion), fungus_mt (fungus mitochondrion), "
                                 "fungus_nr (fungus nuclear ribosomal RNA), "
                                 "or embplant_mt,other_pt,fungus_mt "
                                 "(the combination of any of above organelle genomes split by comma(s), "
                                 "which might be computationally more intensive than separate runs), "
                                 "or anonym (uncertain organelle genome type). "
                                 "The anonym should be used with customized seed and label databases "
                                 "('-s' and '--genes').")
        parser.add_argument("-g", dest="input_graph", help="Input assembly graph (fastg/gfa) file. "
                                                         "The format will be recognized by the file name suffix.")
        parser.add_argument("-o", dest="output_base", help="Output directory. Overwriting files if directory exists.")
        parser.add_argument('--min-depth', dest='min_depth', default=0., type=float,
                            help='Input a float or integer number. Filter graph file by a minimum depth. Default: %(default)s.')
        parser.add_argument('--max-depth', dest='max_depth', default=inf, type=float,
                            help='Input a float or integer number. filter graph file by a maximum depth. Default: %(default)s.')
        parser.add_argument("--config-dir", dest="get_organelle_path", default=None,
                            help="The directory where the configuration file and default databases were placed. "
                                 "The default value also can be changed by adding 'export GETORG_PATH=your_favor' "
                                 "to the shell script (e.g. ~/.bash_profile or ~/.bashrc) "
                                 "Default: " + GO_PATH)
        parser.add_argument("--genes", dest="genes_fasta",
                            help="Followed with a customized database (a fasta file or the base name of a "
                                 "blast database) containing or made of ONE set of protein coding genes "
                                 "and ribosomal RNAs extracted from ONE reference genome that you want to assemble. "
                                 "Should be a list of databases split by comma(s) on a multi-organelle mode, "
                                 "with the same list length to organelle_type (followed by '-F'). "
                                 "This is optional for any organelle mentioned in '-F' but required for 'anonym'. "
                                 "By default, certain database(s) in " + str(LBL_DB_PATH) + " would be used "
                                 "contingent on the organelle types chosen (-F). "
                                 "The default value no longer holds when '--genes' or '--ex-genes' is used.")
        parser.add_argument("--ex-genes", dest="exclude_genes",
                            help="This is optional and Not suggested, since non-target contigs could contribute "
                                 "information for better downstream coverage-based clustering. "
                                 "Followed with a customized database (a fasta file or the base name of a "
                                 "blast database) containing or made of protein coding genes "
                                 "and ribosomal RNAs extracted from reference genome(s) that you want to exclude. "
                                 "Could be a list of databases split by comma(s) but "
                                 "NOT required to have the same list length to organelle_type (followed by '-F'). "
                                 "The default value no longer holds when '--genes' or '--ex-genes' is used.")
        parser.add_argument("--no-slim", dest="no_slim", default=False, action="store_true",
                            help="Disable slimming process and directly disentangle the original assembly graph. "
                                 "Default: %(default)s")
        parser.add_argument("--slim-options", dest="slim_options", default="",
                            help="Other options for calling slim_graph.py")
        parser.add_argument("--max-slim-extending-len", dest="max_slim_extending_len", default=None, type=float,
                            help="This is used to limit the extending length, below which a \"non-hit contig\" is allowed "
                                 "to be distant from a \"hit contig\" to be kept. "
                                 "See more under slim_graph.py:--max-slim-extending-len. "
                                 "Default: " +
                                 str(MAX_SLIM_EXTENDING_LENS["embplant_pt"]) + " (-F embplant_pt), " +
                                 str(MAX_SLIM_EXTENDING_LENS["embplant_mt"]) + " (-F embplant_mt/fungus_mt/other_pt), " +
                                 str(MAX_SLIM_EXTENDING_LENS["embplant_nr"]) + " (-F embplant_nr/fungus_nr/animal_mt), "
                                 "maximum_of_type1_type2 (-F type1,type2), inf (-F anonym)")
        parser.add_argument("--spades-out-dir", dest="spades_scaffolds_path",
                            help="Input spades output directory with 'scaffolds.fasta' and 'scaffolds.paths', which are "
                                 "used for scaffolding disconnected contigs with GAPs. Default: disabled")
        parser.add_argument("--depth-factor", dest="depth_factor", default=5.0, type=float,
                            help="Depth factor for differentiate genome type of contigs. "
                                 "The genome type of contigs are determined by blast. "
                                 "Default: %(default)s")
        parser.add_argument("--type-f", dest="type_factor", type=float, default=3.,
                            help="Type factor for identifying contig type tag when multiple tags exist in one contig. "
                                 "Default:%(default)s")
        parser.add_argument("--weight-f", dest="weight_factor", type=float, default=100.0,
                            help="weight factor for excluding isolated/terminal suspicious contigs with gene labels. "
                                 "Default:%(default)s")
        parser.add_argument("--contamination-depth", dest="contamination_depth", default=3., type=float,
                            help="Depth factor for confirming contamination in parallel contigs. Default: %(default)s")
        parser.add_argument("--contamination-similarity", dest="contamination_similarity", default=0.9, type=float,
                            help="Similarity threshold for confirming contaminating contigs. Default: %(default)s")
        parser.add_argument("--no-degenerate", dest="degenerate", default=True, action="store_false",
                            help="Disable making consensus from parallel contig based on nucleotide degenerate table.")
        parser.add_argument("--degenerate-depth", dest="degenerate_depth", default=1.5, type=float,
                            help="Depth factor for confirming parallel contigs. Default: %(default)s")
        parser.add_argument("--degenerate-similarity", dest="degenerate_similarity", default=0.98, type=float,
                            help="Similarity threshold for confirming parallel contigs. Default: %(default)s")
        parser.add_argument("--disentangle-time-limit", dest="disentangle_time_limit", default=3600, type=int,
                            help="Time limit (second) for each try of disentangling a graph file as a circular "
                                 "genome. Disentangling a graph as contigs is not limited. Default: %(default)s")
        parser.add_argument("--expected-max-size", dest="expected_max_size", default='200000', type=str,
                            help="Expected maximum target genome size(s) for disentangling. "
                                 "Should be a list of INTEGER numbers split by comma(s) on a multi-organelle mode, "
                                 "with the same list length to organelle_type (followed by '-F'). "
                                 "Default: 250000 (-F embplant_pt/fungus_mt), 25000 (-F embplant_nr/fungus_nr/animal_mt), "
                                 "1000000 (-F embplant_mt/other_pt), "
                                 "1000000,1000000,250000 (-F other_pt,embplant_mt,fungus_mt)")
        parser.add_argument("--expected-min-size", dest="expected_min_size", default=10000, type=int,
                            help="Expected minimum target genome size(s) for disentangling. "
                                 "Should be a list of INTEGER numbers split by comma(s) on a multi-organelle mode, "
                                 "with the same list length to organelle_type (followed by '-F'). "
                                 "Default: %(default)s for all.")
        parser.add_argument("--reverse-lsc", dest="reverse_lsc", default=False, action="store_true",
                            help="For '-F embplant_pt' with complete circular result, "
                                 "by default, the direction of the starting contig (usually "
                                 "the LSC contig) is determined as the direction with less ORFs. Choose this option "
                                 "to reverse the direction of the starting contig when result is circular. "
                                 "Actually, both directions are biologically equivalent to each other. The "
                                 "reordering of the direction is only for easier downstream analysis.")
        parser.add_argument("--max-paths-num", dest="max_paths_num", default=1000, type=int,
                            help="Repeats would dramatically increase the number of potential isomers (paths). "
                                 "This option was used to export a certain amount of paths out of all possible paths "
                                 "per assembly graph. Default: %(default)s")
        parser.add_argument("--keep-all-polymorphic", dest="only_keep_max_cov", default=True, action="store_false",
                            help="By default, this script would pick the contig with highest coverage among all parallel "
                                 "(polymorphic) contigs when degenerating was not applicable. "
                                 "Choose this flag to export all combinations.")
        parser.add_argument("--min-sigma", dest="min_sigma_factor", type=float, default=0.1,
                            help="Minimum deviation factor for excluding non-target contigs. Default:%(default)s")
        # parser.add_argument("--max-multiplicity", dest="max_multiplicity", type=int, default=8,
        #                     help="Maximum multiplicity of contigs for disentangling genome paths. "
        #                          "Should be 1~12. Default:%(default)s")
        parser.add_argument("-t", dest="threads", type=int, default=1,
                            help="Maximum threads to use.")
        parser.add_argument("--prefix", dest="prefix", default="",
                            help="Add extra prefix to resulting files under the output directory.")
        parser.add_argument("--which-blast", dest="which_blast", default="",
                            help="Assign the path to BLAST binary files if not added to the path. "
                                 "Default: try \"" + os.path.realpath(GO_DEP_PATH) +
                                 "/ncbi-blast\" first, then $PATH")
        parser.add_argument("--which-bandage", dest="which_bandage", default="",
                            help="Assign the path to bandage binary file if not added to the path. Default: try $PATH")
        parser.add_argument("--keep-temp", dest="keep_temp_files", action="store_true", default=False,
                            help="Choose to keep the running temp/index files.")
        parser.add_argument("--continue", dest="script_resume", default=False, action="store_true",
                            help="Several check points based on files produced, rather than on the log file, "
                                 "so keep in mind that this script will not detect the difference "
                                 "between this input parameters and the previous ones.")
        parser.add_argument("--overwrite", dest="script_overwrite", default=False, action="store_true",
                            help="Overwrite previous file if existed. ")
        parser.add_argument("--random-seed", dest="random_seed", default=12345, type=int,
                            help="Default: %(default)s")
        parser.add_argument("-v", "--version", action="version", version="GetOrganelle v{version}".format(version=version))
        parser.add_argument("--verbose", dest="verbose_log", action="store_true", default=False,
                            help="Verbose output. Choose to enable verbose running log_handler.")
        parser.add_argument("-h", dest="simple_help", default=False, action="store_true",
                            help="print brief introduction for frequently-used options.")
        parser.add_argument("--help", dest="verbose_help", default=False, action="store_true",
                            help="print verbose introduction for all options.")
        if "--help" in sys.argv:
            parser.print_help()
            exit()

    # redirect organelle types before parsing arguments
    redirect_organelle_types = {"plant_cp": "embplant_pt",
                                "plant_pt": "embplant_pt",
                                "plant_mt": "embplant_mt",
                                "plant_nr": "embplant_nr"}
    for go_arg, candidate_arg in enumerate(sys.argv):
        if go_arg > 1 and sys.argv[go_arg - 1] in {"-F", "-E"}:
            if candidate_arg in redirect_organelle_types:
                sys.argv[go_arg] = redirect_organelle_types[candidate_arg]
            elif "," in candidate_arg:
                new_arg = []
                for sub_arg in candidate_arg.split(","):
                    if sub_arg in redirect_organelle_types:
                        new_arg.append(redirect_organelle_types[sub_arg])
                    else:
                        new_arg.append(sub_arg)
                sys.argv[go_arg] = ",".join(new_arg)
    #
    try:
        options = parser.parse_args()
    except Exception as e:
        sys.stdout.write("\n############################################################################\n" + str(e))
        sys.stdout.write("\n\"-h\" for more usage")
        exit()
    else:
        if not options.output_base:
            sys.stdout.write("\n############################################################################"
                             "\nERROR: Insufficient arguments!\n")
            sys.stdout.write("Missing option: output directory (followed after '-o')!\n")
            exit()
        if not options.input_graph:
            sys.stdout.write("\n############################################################################"
                             "\nERROR: Insufficient arguments!\n")
            sys.stdout.write("Missing option: input assembly graph (followed after '-g')!\n")
            exit()
        if not options.organelle_type:
            sys.stdout.write("\n############################################################################"
                             "\nERROR: Insufficient arguments!\n")
            sys.stdout.write("Missing option: organelle type (followed after '-F')!\n")
            exit()
        elif options.no_slim:
            if "," in options.organelle_type:
                sys.stderr.write("\n############################################################################"
                                 "\nMultiple organelle types not allowed for \"--no-slim\" mode!\n")
                exit()
            else:
                options.organelle_type = options.organelle_type.split(",")
        else:
            options.organelle_type = options.organelle_type.split(",")

        global _GO_PATH, _LBL_DB_PATH, _SEQ_DB_PATH
        if options.get_organelle_path:
            _GO_PATH = os.path.expanduser(options.get_organelle_path)
            if os.path.isdir(_GO_PATH):
                _LBL_DB_PATH = os.path.join(_GO_PATH, LBL_NAME)
                _SEQ_DB_PATH = os.path.join(_GO_PATH, SEQ_NAME)
            else:
                sys.stdout.write("\n############################################################################"
                                 "\nERROR: path " + _GO_PATH + " invalid!\n")
                exit()

        def _check_default_db(this_sub_organelle, extra_type=""):
            if not (os.path.isfile(os.path.join(_LBL_DB_PATH, this_sub_organelle + ".fasta")) or options.genes_fasta):
                sys.stdout.write("\n############################################################################"
                                 "\nERROR: default " + this_sub_organelle + "," * int(bool(extra_type)) + extra_type +
                                 " database not added yet!\n"
                                  "These two types must be used together!\n" * int(bool(extra_type)) +
                                 "\nInstall it(them) by: get_organelle_config.py -a " + this_sub_organelle +
                                 "," * int(bool(extra_type)) + extra_type +
                                 "\nor\nInstall all types by: get_organelle_config.py -a all\n")
                exit()
        for sub_organelle_t in options.organelle_type:
            if sub_organelle_t not in {"embplant_pt", "other_pt", "embplant_mt", "embplant_nr", "animal_mt",
                                       "fungus_mt", "fungus_nr", "anonym"}:
                sys.stdout.write("\n############################################################################"
                                 "\nERROR: \"-F\" MUST be one of 'embplant_pt', 'other_pt', 'embplant_mt', "
                                 "'embplant_nr', 'animal_mt', 'fungus_mt', 'fungus_nr', 'anonym', or a "
                                 "combination of above split by comma(s)!\n\n")
                exit()
            elif sub_organelle_t == "anonym":
                if not (options.genes_fasta or options.no_slim):
                    sys.stdout.write("\n############################################################################"
                                     "\nERROR: \"--genes\" or \"--no-slim\" should be used when \"-F anonym\"!\n\n")
                    exit()
            else:
                if sub_organelle_t in ("embplant_pt", "embplant_mt"):
                    for go_t, check_sub in enumerate(["embplant_pt", "embplant_mt"]):
                        _check_default_db(check_sub, ["embplant_pt", "embplant_mt"][not go_t])
                else:
                    _check_default_db(sub_organelle_t)

        if options.spades_scaffolds_path:
            if not os.path.isdir(options.spades_scaffolds_path):
                raise FileNotFoundError(options.spades_scaffolds_path + " not accessible as a directory!")
            scaffold_fasta = os.path.join(options.spades_scaffolds_path, "scaffolds.fasta")
            if not os.path.exists(scaffold_fasta):
                raise FileNotFoundError(scaffold_fasta + " not found!")
            scaffold_paths = os.path.join(options.spades_scaffolds_path, "scaffolds.paths")
            if not os.path.exists(scaffold_paths):
                raise FileNotFoundError(scaffold_paths + " not found!")
        assert options.threads > 0
        # assert 12 >= options.max_multiplicity >= 1
        assert options.max_paths_num > 0
        assert options.script_resume + options.script_overwrite < 2, "'--overwrite' conflicts with '--continue'"
        organelle_type_len = len(options.organelle_type)
        options.prefix = os.path.basename(options.prefix)

        if os.path.isdir(options.output_base):
            if options.script_resume:
                pass
            else:
                if options.script_overwrite:
                    try:
                        rmtree(options.output_base)
                    except OSError as e:
                        sys.stderr.write(
                            "\n############################################################################"
                            "\nRemoving existed " + options.output_base + " failed! "
                            "\nPlease manually remove it or use a new output directory!\n")
                    os.mkdir(options.output_base)
                else:
                    sys.stderr.write("\n############################################################################"
                                     "\n" + options.output_base + " existed! "
                                     "\nPlease use a new output directory, or use '--continue'/'--overwrite'\n")
                    exit()
        else:
            options.script_resume = False
            os.mkdir(options.output_base)

        log_handler = simple_log(logging.getLogger(), options.output_base, options.prefix + "get_org.")
        log_handler.info("")
        log_handler.info(description)
        log_handler.info("Python " + str(sys.version).replace("\n", " "))
        log_handler.info("PLATFORM: " + " ".join(platform.uname()))
        # log versions of dependencies
        lib_versions_info = list()
        lib_versions_info.append("GetOrganelleLib " + GetOrganelleLib.__version__)
        try:
            import numpy as np
        except ImportError:
            log_handler.error("numpy is not available! Please install numpy!")
            sys.exit()
        else:
            lib_versions_info.append("numpy " + np.__version__)
        # try:
        #     import sympy
        # except ImportError:
        #     log_handler.error("sympy is not available! Please install sympy!")
        #     sys.exit()
        # else:
        #     lib_versions_info.append("sympy " + sympy.__version__)
        try:
            import gekko
        except ImportError:
            log_handler.error("gekko is not available! Please install gekko!")
            sys.exit()
        else:
            lib_versions_info.append("gekko " + gekko.__version__)
        log_handler.info("PYTHON LIBS: " + "; ".join(lib_versions_info))
        dep_versions_info = []
        if not options.no_slim:
            options.which_blast = detect_blast_path(options.which_blast, GO_DEP_PATH)
            if executable(os.path.join(options.which_blast, "blastn")):
                dep_versions_info.append(detect_blast_version(options.which_blast))
            else:
                log_handler.error(os.path.join(options.which_blast, "blastn") + " not accessible!")
                exit()
        if options.genes_fasta and not executable(os.path.join(options.which_blast, "makeblastdb")):
            log_handler.error(os.path.join(options.which_blast, "makeblastdb") + " not accessible!")
            exit()
        if executable(os.path.join(options.which_bandage, "Bandage -v")):
            dep_versions_info.append(detect_bandage_version(options.which_bandage))
        log_handler.info("DEPENDENCIES: " + "; ".join(dep_versions_info))
        log_handler.info("GETORG_PATH=" + _GO_PATH)
        # existing default database
        if not options.no_slim:
            existing_seed_db, existing_label_db = get_current_db_versions(db_type="both", seq_db_path=_SEQ_DB_PATH,
                                                                          lbl_db_path=_LBL_DB_PATH, silent=True)
            log_types = ["" if options.genes_fasta else this_type for this_type in options.organelle_type]
            if "embplant_pt" in log_types and "embplant_mt" not in log_types:
                log_types.append("embplant_mt")
            if "embplant_mt" in log_types and "embplant_pt" not in log_types:
                log_types.append("embplant_pt")
            log_handler.info("LABEL DB: " + single_line_db_versions(existing_label_db, log_types))
        # working directory
        log_handler.info("WORKING_DIR=" + os.getcwd())
        log_handler.info(" ".join(["\"" + arg + "\"" if " " in arg else arg for arg in sys.argv]) + "\n")

        assert is_valid_path(os.path.realpath(options.output_base)), \
            "Invalid characters (e.g. space, non-ascii) for SPAdes in path: " + os.path.realpath(options.output_base)
        assert is_valid_path(options.prefix), \
            "Invalid characters (e.g. space, non-ascii) for SPAdes in prefix: " + options.prefix

        log_handler = timed_log(log_handler, options.output_base, options.prefix + "get_org.")

        # using the default
        if "--genes" not in sys.argv:
            options.genes_fasta = []  # None] * organelle_type_len
        else:
            temp_val_len = len(str(options.genes_fasta).split(","))
            if temp_val_len != organelle_type_len:
                log_handler.error("-F is followed with " + str(organelle_type_len) + " organelle types, " +
                                  "while --genes is followed with " + str(temp_val_len) + " value(s)!\n")
                exit()
            temp_vals = []
            for sub_genes in str(options.genes_fasta).split(","):
                # if sub_genes == "":
                #     temp_vals.append(sub_genes)
                if not (os.path.exists(sub_genes) or os.path.exists(remove_db_postfix(sub_genes) + ".nhr")):
                    log_handler.error(sub_genes + " not found!")
                    exit()
                else:
                    temp_vals.append(sub_genes)
            options.genes_fasta = temp_vals
        if "--ex-genes" not in sys.argv:
            options.exclude_genes = []
        else:
            temp_vals = []
            for sub_genes in str(options.exclude_genes).split(","):
                if not (os.path.exists(sub_genes) or os.path.exists(remove_db_postfix(sub_genes) + ".nhr")):
                    log_handler.error(sub_genes + " not found!")
                    exit()
                else:
                    temp_vals.append(sub_genes)
            options.exclude_genes = temp_vals

        if "--expected-max-size" not in sys.argv:
            raw_default_value = int(str(options.expected_max_size))
            options.expected_max_size = []
            for got_t, sub_organelle_t in enumerate(options.organelle_type):
                if sub_organelle_t == "embplant_pt":
                    options.expected_max_size.append(raw_default_value)
                elif sub_organelle_t == "embplant_mt":
                    options.expected_max_size.append(int(raw_default_value * 4))
                elif sub_organelle_t == "fungus_mt":
                    options.expected_max_size.append(raw_default_value)
                elif sub_organelle_t in ("embplant_nr", "fungus_nr", "animal_mt"):
                    options.expected_max_size.append(int(raw_default_value / 10))
                elif sub_organelle_t == "anonym":
                    if options.genes_fasta:
                        ref_seqs = read_fasta(options.genes_fasta[got_t])[1]
                        options.expected_max_size.append(10 * sum([len(this_seq) for this_seq in ref_seqs]))
                        log_handler.info("Setting '--expected-max-size " + str(options.expected_max_size) +
                                        "' for estimating the word size value for anonym type.")
                    else:
                        options.expected_max_size.append(inf)
        else:
            temp_val_len = len(str(options.expected_max_size).split(","))
            if temp_val_len != organelle_type_len:
                log_handler.error("-F is followed with " + str(organelle_type_len) + " organelle types, " +
                                  "while --expected-max-size is followed with " + str(temp_val_len) + " value(s)!\n")
                exit()
            try:
                options.expected_max_size = [int(sub_size) for sub_size in str(options.expected_max_size).split(",")]
            except ValueError:
                log_handler.error("Invalid --expected-max-size value(s): " + str(options.expected_max_size))
                exit()

        if "--expected-min-size" not in sys.argv:
            raw_default_value = int(str(options.expected_min_size))
            options.expected_min_size = []
            for sub_organelle_t in options.organelle_type:
                options.expected_min_size.append(raw_default_value)
        else:
            temp_val_len = len(str(options.expected_min_size).split(","))
            if temp_val_len != organelle_type_len:
                log_handler.error("-F is followed with " + str(organelle_type_len) + " organelle types, " +
                                  "while --expected-min-size is followed with " + str(temp_val_len) + " value(s)!\n")
                exit()
            try:
                options.expected_min_size = [int(sub_size) for sub_size in str(options.expected_min_size).split(",")]
            except ValueError:
                log_handler.error("Invalid --expected-min-size value(s): " + str(options.expected_min_size))
                exit()
        # check slim options
        if options.slim_options.strip():
            slim_op_parts = options.slim_options.split()
            ban_argv = {"-F": 2, "-E": 2, "--min-depth": 2, "--max-depth": 2, "--merge": 1, "--wrapper": 1,
                        "--include": 2, "--include-priority": 2, "--exclude": 2, "--exclude-priority": 2,
                        "--no-hits-labeled-tab": 1, "-o": 2, "--prefix": 2, "--out-base": 2, "--log": 1,
                        "--verbose": 1, "--continue": 1, "--no-overwrite": 1, "--which-blast": 2, "-t": 2,
                        "--threads": 2, "--max-slim-extending-len": 2}
            remove_ops = []
            go_op = 0
            while go_op < len(slim_op_parts):
                if slim_op_parts[go_op] in ban_argv:
                    for repeat_time in range(ban_argv[slim_op_parts[go_op]]):
                        remove_ops.append(slim_op_parts.pop(go_op))
                else:
                    go_op += 1
            if remove_ops:
                log_handler.info("Options \"" + " ".join(remove_ops) +
                                 "\" taken/invalid for wrapped slim_graph.py, removed.")
                options.slim_options = " ".join(slim_op_parts)
        # random.seed(options.random_seed)
        # np.random.seed(options.random_seed)
        return options, log_handler


def slim_assembly_graph(organelle_types, in_custom, ex_custom, graph_in, graph_out_base, max_slim_extending_len,
                        verbose_log, log_handler, threads, which_slim, which_blast="", other_options="",
                        resume=False, keep_temp=False):
    include_priority_db = []
    exclude_db = []
    if in_custom or ex_custom:
        include_priority_db = in_custom
        exclude_db = ex_custom
    else:
        if organelle_types == ["embplant_pt"]:
            include_priority_db = [os.path.join(_LBL_DB_PATH, "embplant_pt.fasta"),
                                   os.path.join(_LBL_DB_PATH, "embplant_mt.fasta")]
            max_slim_extending_len = max_slim_extending_len if max_slim_extending_len else MAX_SLIM_EXTENDING_LENS[organelle_types[0]]
        elif organelle_types == ["embplant_mt"]:
            include_priority_db = [os.path.join(_LBL_DB_PATH, "embplant_mt.fasta"),
                                   os.path.join(_LBL_DB_PATH, "embplant_pt.fasta")]
            max_slim_extending_len = max_slim_extending_len if max_slim_extending_len else MAX_SLIM_EXTENDING_LENS[organelle_types[0]]
        else:
            include_priority_db = [os.path.join(_LBL_DB_PATH, sub_organelle_t + ".fasta")
                                   for sub_organelle_t in organelle_types]
            if max_slim_extending_len is None:
                max_slim_extending_len = max([MAX_SLIM_EXTENDING_LENS[sub_organelle_t]
                                         for sub_organelle_t in organelle_types])
    if resume:
        if os.path.exists(graph_out_base + "." + graph_in.split(".")[-1]) and os.path.exists(graph_out_base + ".csv"):
            if log_handler:
                log_handler.info("Slimming " + graph_in + " ... skipped.")
            return 0
    run_command = ""
    if include_priority_db:
        run_command += " --include-priority " + ",".join(include_priority_db)
    if exclude_db:
        run_command += " --exclude " + ",".join(exclude_db)
    which_bl_str = " --which-blast " + which_blast if which_blast else ""
    run_command = os.path.join(which_slim, "slim_graph.py") + " -t " + str(threads) + which_bl_str + \
                  " " + graph_in + " --out-base " + graph_out_base + " " + run_command + " --log --wrapper " + \
                  "--verbose " * int(bool(verbose_log)) + "--continue " * int(bool(resume)) + other_options + \
                  (" --max-slim-extending-len " + str(max_slim_extending_len) + " ") * int(bool(max_slim_extending_len)) + \
                  " --keep-temp" * int(bool(keep_temp))
    # + ' -o ' + out_base + (' --prefix ' + prefix if prefix else "")
    slim_spades = subprocess.Popen(run_command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
    if verbose_log and log_handler:
        log_handler.info(run_command)
    output, err = slim_spades.communicate()
    # if "not recognized" in output.decode("utf8") or "command not found" in output.decode("utf8") \
    #         or "no such file" in output.decode("utf8"):
    #     if log_handler:
    #         log_handler.error("Slimming " + graph_in + " failed.")
    #     return os.path.join(which_slim, "slim_graph.py") + " not accessible!\n" + output.decode("utf8").strip()
    if " failed" in output.decode("utf8") or " - ERROR" in output.decode("utf8") or \
            "slim_graph.py: error" in output.decode("utf8"):
        if log_handler:
            log_handler.error("Slimming " + graph_in + " failed. "
                              "Please check *slim.log.txt for details. ")
        return "\n" + output.decode("utf8").strip()
    else:
        if log_handler:
            if verbose_log:
                log_handler.info(output.decode("utf8"))
            log_handler.info("Slimming " + graph_in + " finished!")
        return 0


def extract_organelle_genome(out_base, slim_out_fg, slim_out_csv, organelle_prefix, organelle_type, blast_db,
                             verbose, log_handler, expected_maximum_size, expected_minimum_size, no_slim, options):
    from GetOrganelleLib.assembly_parser import Assembly, ProcessingGraphFailed
    import random
    random.seed(options.random_seed)

    # import numpy as np

    # testing random effect
    # import random as rd_standard
    #
    # np.random.seed(options.random_seed)
    # class test_random:
    #     def __init__(self):
    #         rd_standard.seed(options.random_seed)
    #         self.rd = rd_standard
    #     def random(self):
    #         print("random", self.rd.random())
    #         return self.rd.random()
    #     def choice(self, *vars, **kwargs):
    #         print("choice", self.rd.random())
    #         return self.rd.choice(*vars, **kwargs)
    #     def choices(self, *vars, **kwargs):
    #         print("choices", self.rd.random())
    #         return self.rd.choices(*vars, **kwargs)
    # random = test_random()

    def disentangle_assembly(assembly_obj, fastg_file, tab_file, output, weight_factor, log_dis, time_limit,
                             type_factor=3.,
                             mode="embplant_pt", blast_db_base="embplant_pt", contamination_depth=3.,
                             contamination_similarity=0.95, degenerate=True,
                             degenerate_depth=1.5, degenerate_similarity=0.98,
                             expected_max_size=inf, expected_min_size=0, hard_cov_threshold=10.,
                             min_sigma_factor=0.1,  # here_max_copy=10,
                             here_only_max_c=True, spades_scaffolds_path=None, here_acyclic_allowed=False,
                             here_verbose=False, timeout_flag_str="'--disentangle-time-limit'", temp_graph=None):
        @set_time_limit(time_limit, flag_str=timeout_flag_str)
        def disentangle_inside(input_graph, fastg_f, tab_f, o_p, w_f, log_in, type_f=3., mode_in="embplant_pt",
                               in_db_n="embplant_pt", c_d=3., c_s=0.95, deg=True, deg_dep=1.5, deg_sim=0.98,
                               hard_c_t=10., min_s_f=0.1, max_cov_in=True,
                               max_s=inf, min_s=0, spades_scaffold_p_in=None,
                               acyclic_allowed_in=False, verbose_in=False, in_temp_graph=None):
            if spades_scaffold_p_in is not None:
                log_in.info("Scaffolding disconnected contigs using SPAdes scaffolds ... ")
                log_in.warning("Assembly based on scaffolding may not be as accurate as "
                               "the ones directly exported from the assembly graph.")
            if acyclic_allowed_in:
                log_in.info("Disentangling " + fastg_f + " as a/an " + in_db_n + "-insufficient graph ... ")
            else:
                log_in.info("Disentangling " + fastg_f + " as a circular genome ... ")
            image_produced = False
            # input_graph = Assembly(fastg_f)
            if spades_scaffold_p_in is not None:
                if not input_graph.add_gap_nodes_with_spades_res(os.path.join(spades_scaffold_p_in, "scaffolds.fasta"),
                                                                 os.path.join(spades_scaffold_p_in, "scaffolds.paths"),
                                                                 min_cov=options.min_depth, max_cov=options.max_depth,
                                                                 log_handler=log_handler):
                    raise ProcessingGraphFailed("No new connections.")
                else:
                    log_handler.info("Re-loading labels along " + slim_out_fg)
                    input_graph.parse_tab_file(
                        tab_f,
                        database_name=in_db_n,
                        type_factor=type_f,
                        max_gene_gap=250,
                        max_cov_diff=hard_c_t,  # contamination_depth?
                        verbose=verbose,
                        log_handler=log_handler,
                        random_obj=random)
                    if in_temp_graph:
                        if in_temp_graph.endswith(".gfa"):
                            this_tmp_graph = in_temp_graph[:-4] + ".scaffolds.gfa"
                        else:
                            this_tmp_graph = in_temp_graph + ".scaffolds.gfa"
                        input_graph.write_to_gfa(this_tmp_graph)
            if no_slim:
                new_average_cov = \
                    input_graph.estimate_copy_and_depth_by_cov(mode=mode_in, log_handler=log_in, verbose=verbose_in)
                target_results = input_graph.estimate_copy_and_depth_precisely(
                    expected_average_cov=new_average_cov,
                    # broken_graph_allowed=acyclic_allowed_in,
                    verbose=verbose_in,
                    log_handler=log_in)
                log_target_res(target_results,
                               log_handler=log_handler,
                               universal_overlap=bool(input_graph.uni_overlap()),
                               mode=mode_in)
            else:
                selected_graph = o_p + ".graph.selected_graph.gfa"
                target_results = input_graph.find_target_graph(mode=mode_in, db_name=in_db_n,  # type_factor=type_f,
                                                               hard_cov_threshold=hard_c_t,
                                                               contamination_depth=c_d,
                                                               contamination_similarity=c_s,
                                                               degenerate=deg, degenerate_depth=deg_dep,
                                                               degenerate_similarity=deg_sim,
                                                               expected_max_size=max_s, expected_min_size=min_s,
                                                               only_keep_max_cov=max_cov_in,
                                                               min_sigma_factor=min_s_f,
                                                               weight_factor=w_f,
                                                               broken_graph_allowed=acyclic_allowed_in,
                                                               log_handler=log_in, verbose=verbose_in,
                                                               temp_graph=in_temp_graph,
                                                               selected_graph=selected_graph,
                                                               random_obj=random)
            if not target_results:
                raise ProcessingGraphFailed("No target graph detected!")
            if len(target_results) > 1:
                log_in.warning(str(len(target_results)) + " sets of graph detected!")
            # log_in.info("Slimming and disentangling graph finished!")

            log_in.info("Writing output ...")
            ambiguous_base_used = False
            if acyclic_allowed_in:
                contig_num = set()
                still_complete = []
                for go_res, res in enumerate(target_results):
                    go_res += 1
                    broken_graph = res["graph"]
                    count_path = 0
                    # use options.max_paths_num + 1 to trigger the warning
                    these_paths = broken_graph.get_all_paths(mode=mode_in, log_handler=log_in,
                                                             max_paths_num=options.max_paths_num + 1)
                    # reducing paths
                    if len(these_paths) > options.max_paths_num:
                        log_in.warning("Only exporting " + str(options.max_paths_num) + " out of all " +
                                       str(options.max_paths_num) +
                                       "+ possible paths. (see '--max-paths-num' to change it.)")
                        these_paths = these_paths[:options.max_paths_num]

                    # exporting paths, reporting results
                    for this_paths, other_tag in these_paths:
                        count_path += 1
                        all_contig_str = []
                        contig_num.add(len(this_paths))
                        contigs_are_circular = []
                        for go_contig, this_p_part in enumerate(this_paths):
                            this_contig = broken_graph.export_path(this_p_part)
                            if DEGENERATE_BASES & set(this_contig.seq):
                                ambiguous_base_used = True
                            if this_contig.label.endswith("(circular)"):
                                contigs_are_circular.append(True)
                            else:
                                contigs_are_circular.append(False)
                            if len(this_paths) == 1 and contigs_are_circular[-1]:
                                all_contig_str.append(this_contig.fasta_str())
                            else:
                                all_contig_str.append(">contig_" + str(go_contig + 1) + "--" + this_contig.label +
                                                      "\n" + this_contig.seq + "\n")

                        if len(all_contig_str) == 1 and set(contigs_are_circular) == {True}:
                            if "GAP" in all_contig_str:
                                still_complete.append("nearly-complete")
                            else:
                                still_complete.append("complete")
                                # print ir stat
                                if count_path == 1 and in_db_n == "embplant_pt":
                                    detect_seq = broken_graph.export_path(this_paths[0]).seq
                                    ir_stats = detect_plastome_architecture(detect_seq, 1000)
                                    log_in.info("Detecting large repeats (>1000 bp) in PATH1 with " + ir_stats[-1] +
                                                ", Total:LSC:SSC:Repeat(bp) = " + str(len(detect_seq)) + ":" +
                                                ":".join([str(len_val) for len_val in ir_stats[:3]]))
                        else:
                            still_complete.append("incomplete")

                        if still_complete[-1] == "complete":
                            out_n = o_p + ".complete.graph" + str(go_res) + "." + \
                                    str(count_path) + other_tag + ".path_sequence.fasta"
                            log_in.info("Writing PATH" + str(count_path) + " of complete " + mode_in + " to " + out_n)
                        elif still_complete[-1] == "nearly-complete":
                            out_n = o_p + ".nearly-complete.graph" + str(go_res) + "." + \
                                    str(count_path) + other_tag + ".path_sequence.fasta"
                            log_in.info(
                                "Writing PATH" + str(count_path) + " of nearly-complete " + mode_in + " to " + out_n)
                        else:
                            out_n = o_p + ".scaffolds.graph" + str(go_res) + other_tag + "." + \
                                    str(count_path) + ".path_sequence.fasta"
                            log_in.info("Writing PATH" + str(count_path) + " of " + mode_in +
                                        " scaffold(s) to " + out_n)
                        open(out_n, "w").write("\n".join(all_contig_str))
                    if set(still_complete[-len(these_paths):]) == {"complete"}:
                        this_out_base = o_p + ".complete.graph" + str(go_res) + ".path_sequence."
                        log_in.info("Writing GRAPH to " + this_out_base + "gfa")
                        broken_graph.write_to_gfa(this_out_base + "gfa")
                        image_produced = draw_assembly_graph_using_bandage(
                            input_graph_file=this_out_base + "gfa", output_image_file=this_out_base + "png",
                            assembly_graph_ob=broken_graph, log_handler=log_handler, verbose_log=verbose_in,
                            which_bandage=options.which_bandage)
                    elif set(still_complete[-len(these_paths):]) == {"nearly-complete"}:
                        this_out_base = o_p + ".nearly-complete.graph" + str(go_res) + ".path_sequence."
                        log_in.info("Writing GRAPH to " + this_out_base + "gfa")
                        broken_graph.write_to_gfa(this_out_base + "gfa")
                        image_produced = draw_assembly_graph_using_bandage(
                            input_graph_file=this_out_base + "gfa", output_image_file=this_out_base + "png",
                            assembly_graph_ob=broken_graph, log_handler=log_handler, verbose_log=verbose_in,
                            which_bandage=options.which_bandage)
                    else:
                        this_out_base = o_p + ".contigs.graph" + str(go_res) + ".path_sequence."
                        log_in.info("Writing GRAPH to " + this_out_base + "gfa")
                        broken_graph.write_to_gfa(this_out_base + "gfa")
                        # image_produced = draw_assembly_graph_using_bandage(
                        #     input_graph_file=this_out_base + "gfa", output_image_file=this_out_base + "png",
                        #     assembly_graph_ob=broken_graph, log_handler=log_handler, verbose_log=verbose_in,
                        #     which_bandage=options.which_bandage)
                if set(still_complete) == {"complete"}:
                    log_in.info("Result status of " + mode_in + ": circular genome")
                elif set(still_complete) == {"nearly-complete"}:
                    log_in.info("Result status of " + mode_in + ": circular genome with gaps")
                else:
                    log_in.info("Result status of " + mode_in + ": " +
                                ",".join(sorted([str(c_n) for c_n in contig_num])) + " scaffold(s)")
            else:
                status_str = "complete"
                for go_res, res in enumerate(target_results):
                    go_res += 1
                    idealized_graph = res["graph"]
                    count_path = 0
                    # use options.max_paths_num + 1 to trigger the warning
                    these_paths = idealized_graph.get_all_circular_paths(
                        mode=mode_in, log_handler=log_in, reverse_start_direction_for_pt=options.reverse_lsc,
                        max_paths_num=options.max_paths_num + 1)

                    # reducing paths
                    if len(these_paths) > options.max_paths_num:
                        log_in.warning("Only exporting " + str(options.max_paths_num) + " out of all " +
                                       str(options.max_paths_num) +
                                       "+ possible paths. (see '--max-paths-num' to change it.)")
                        these_paths = these_paths[:options.max_paths_num]

                    # exporting paths, reporting results
                    for this_path, other_tag in these_paths:
                        count_path += 1
                        this_seq_obj = idealized_graph.export_path(this_path)
                        if DEGENERATE_BASES & set(this_seq_obj.seq):
                            ambiguous_base_used = True
                            status_str = "nearly-complete"
                        out_n = o_p + "." + status_str + ".graph" + str(go_res) + "." + str(
                            count_path) + other_tag + ".path_sequence.fasta"
                        open(out_n, "w").write(this_seq_obj.fasta_str())

                        # print ir stat
                        if count_path == 1 and in_db_n == "embplant_pt" and not ambiguous_base_used:
                            detect_seq = this_seq_obj.seq
                            ir_stats = detect_plastome_architecture(detect_seq, 1000)
                            log_in.info("Detecting large repeats (>1000 bp) in PATH1 with " + ir_stats[-1] +
                                        ", Total:LSC:SSC:Repeat(bp) = " + str(len(detect_seq)) + ":" +
                                        ":".join([str(len_val) for len_val in ir_stats[:3]]))
                        log_in.info(
                            "Writing PATH" + str(count_path) + " of " + status_str + " " + mode_in + " to " + out_n)
                    temp_base_out = o_p + "." + status_str + ".graph" + str(go_res) + ".path_sequence."
                    log_in.info("Writing GRAPH to " + temp_base_out + "gfa")
                    idealized_graph.write_to_gfa(temp_base_out + "gfa")
                    image_produced = draw_assembly_graph_using_bandage(
                        input_graph_file=temp_base_out + "gfa", output_image_file=temp_base_out + "png",
                        assembly_graph_ob=idealized_graph, log_handler=log_handler, verbose_log=verbose_in,
                        which_bandage=options.which_bandage)
                if ambiguous_base_used:
                    log_in.info("Result status of " + mode_in + ": circular genome with gaps")
                else:
                    log_in.info("Result status of " + mode_in + ": circular genome")
            if ambiguous_base_used:
                log_in.warning("Degenerate base(s) used!")
            if not acyclic_allowed_in:
                if slim_out_csv:
                    if image_produced:
                        log_in.info("Please check the produced assembly image"
                                    " or manually visualize " + slim_out_fg + " and load " + slim_out_csv +
                                    " using Bandage to confirm the final result.")
                    else:
                        log_in.info("Please visualize " + slim_out_fg + " and load " + slim_out_csv +
                                    " using Bandage to confirm the final result.")
            log_in.info("Writing output finished.")

        disentangle_inside(input_graph=deepcopy(assembly_obj),
                           fastg_f=fastg_file, tab_f=tab_file, o_p=output, w_f=weight_factor, log_in=log_dis,
                           type_f=type_factor, mode_in=mode, in_db_n=blast_db_base,
                           c_d=contamination_depth, c_s=contamination_similarity,
                           deg=degenerate, deg_dep=degenerate_depth, deg_sim=degenerate_similarity,
                           hard_c_t=hard_cov_threshold, min_s_f=min_sigma_factor,
                           max_cov_in=here_only_max_c,  # max_copy_in=here_max_copy,
                           max_s=expected_max_size, min_s=expected_min_size,
                           acyclic_allowed_in=here_acyclic_allowed, spades_scaffold_p_in=spades_scaffolds_path,
                           verbose_in=here_verbose, in_temp_graph=temp_graph)

    # parsing tab file
    # if meta:
    #     try:
    #         self.parse_tab_file(
    #             tab_file,
    #             database_name=db_name,
    #             type_factor=type_factor,
    #             max_gene_gap=250,
    #             max_cov_diff=hard_cov_threshold,
    #             verbose=verbose,
    #             log_handler=log_handler)
    #     except ProcessingGraphFailed:
    #         return []
    # else:
    # only parsing the assembly obj and tab file once
    log_handler.info("Parsing " + slim_out_fg)
    assembly_graph_obj = Assembly(slim_out_fg, log_handler=log_handler)
    log_handler.info("Loading and cleaning labels along " + slim_out_fg)
    assembly_graph_obj.parse_tab_file(
        slim_out_csv,
        database_name=blast_db,
        type_factor=options.type_factor,
        max_gene_gap=250,
        max_cov_diff=options.depth_factor,  # contamination_depth?
        verbose=verbose,
        log_handler=log_handler,
        random_obj=random)

    # start
    timeout_flag = "'--disentangle-time-limit'"
    export_succeeded = False
    path_prefix = os.path.join(out_base, organelle_prefix)
    graph_temp_file1 = path_prefix + ".temp.R1.gfa" if options.keep_temp_files else None
    try:
        """disentangle"""
        disentangle_assembly(assembly_obj=assembly_graph_obj,
                             fastg_file=slim_out_fg, blast_db_base=blast_db, mode=organelle_type,
                             tab_file=slim_out_csv, output=path_prefix,
                             weight_factor=options.weight_factor, type_factor=options.type_factor,
                             hard_cov_threshold=options.depth_factor,
                             contamination_depth=options.contamination_depth,
                             contamination_similarity=options.contamination_similarity,
                             degenerate=options.degenerate, degenerate_depth=options.degenerate_depth,
                             degenerate_similarity=options.degenerate_similarity,
                             expected_max_size=expected_maximum_size,
                             expected_min_size=expected_minimum_size,
                             # here_max_copy=options.max_multiplicity,
                             here_only_max_c=options.only_keep_max_cov,
                             min_sigma_factor=options.min_sigma_factor,
                             here_acyclic_allowed=False, here_verbose=verbose, log_dis=log_handler,
                             time_limit=options.disentangle_time_limit, timeout_flag_str=timeout_flag,
                             temp_graph=graph_temp_file1)
    except ImportError as e:
        log_handler.error("Disentangling failed: " + str(e))
        return False
    except AttributeError as e:
        if verbose:
            raise e
    except RuntimeError as e:
        log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
    except TimeoutError as e:
        log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
    except ProcessingGraphFailed as e:
        log_handler.info("Disentangling unsuccessful: " + str(e).strip())
    except Exception as e:
        log_handler.exception("")
        raise e
    else:
        export_succeeded = True

    if not export_succeeded and options.spades_scaffolds_path:
        graph_temp_file1s = path_prefix + ".temp.R1S.gfa" if options.keep_temp_files else None
        try:
            """disentangle"""
            disentangle_assembly(assembly_obj=assembly_graph_obj,
                                 fastg_file=slim_out_fg, blast_db_base=blast_db, mode=organelle_type,
                                 tab_file=slim_out_csv, output=path_prefix,
                                 weight_factor=options.weight_factor, type_factor=options.type_factor,
                                 hard_cov_threshold=options.depth_factor,
                                 contamination_depth=options.contamination_depth,
                                 contamination_similarity=options.contamination_similarity,
                                 degenerate=options.degenerate, degenerate_depth=options.degenerate_depth,
                                 degenerate_similarity=options.degenerate_similarity,
                                 expected_max_size=expected_maximum_size,
                                 expected_min_size=expected_minimum_size,
                                 # here_max_copy=options.max_multiplicity,
                                 here_only_max_c=options.only_keep_max_cov,
                                 min_sigma_factor=options.min_sigma_factor,
                                 spades_scaffolds_path=options.spades_scaffolds_path,
                                 here_acyclic_allowed=False, here_verbose=verbose, log_dis=log_handler,
                                 time_limit=options.disentangle_time_limit, timeout_flag_str=timeout_flag,
                                 temp_graph=graph_temp_file1s)
        except ImportError as e:
            log_handler.error("Disentangling failed: " + str(e))
            return False
        except AttributeError as e:
            if verbose:
                raise e
        except RuntimeError as e:
            log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
        except TimeoutError as e:
            log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
        except ProcessingGraphFailed as e:
            log_handler.info("Disentangling unsuccessful: " + str(e).strip())
        except Exception as e:
            log_handler.exception("")
            raise e
        else:
            export_succeeded = True

    if not export_succeeded:
        graph_temp_file2 = path_prefix + ".temp.R2.gfa" if options.keep_temp_files else None
        try:
            """disentangle the graph as scaffold(s)/contig(s)"""
            disentangle_assembly(assembly_obj=assembly_graph_obj,
                                 fastg_file=slim_out_fg, blast_db_base=blast_db, mode=organelle_type,
                                 tab_file=slim_out_csv, output=path_prefix,
                                 weight_factor=options.weight_factor, type_factor=options.type_factor,
                                 here_verbose=verbose, log_dis=log_handler,
                                 hard_cov_threshold=options.depth_factor * 0.6,
                                 # TODO the adjustment should be changed if it's RNA data
                                 contamination_depth=options.contamination_depth,
                                 contamination_similarity=options.contamination_similarity,
                                 degenerate=options.degenerate,
                                 degenerate_depth=options.degenerate_depth,
                                 degenerate_similarity=options.degenerate_similarity,
                                 expected_max_size=expected_maximum_size,
                                 expected_min_size=expected_minimum_size,
                                 min_sigma_factor=options.min_sigma_factor,
                                 # here_max_copy=options.max_multiplicity,
                                 here_only_max_c=options.only_keep_max_cov, here_acyclic_allowed=True,
                                 time_limit=3600, timeout_flag_str=timeout_flag,
                                 temp_graph=graph_temp_file2)
        except (ImportError, AttributeError) as e:
            log_handler.error("Disentangling failed: " + str(e).strip())
        except RuntimeError as e:
            if verbose:
                log_handler.exception("")
            log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
        except TimeoutError as e:
            log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
        except ProcessingGraphFailed as e:
            log_handler.info("Disentangling unsuccessful: " + str(e).strip())
        except Exception as e:
            raise e
        else:
            export_succeeded = True
            if slim_out_csv:
                log_handler.info(
                    "Please visualize " + slim_out_fg + " and load " +
                    slim_out_csv + " to confirm the incomplete result.")
            # log.info("-------------------------------------------------------")
            log_handler.info("If the result is nearly complete, you can try join_spades_fastg_by_blast.py to fill "
                             "N-gaps in-between contigs with a closely-related reference.")
            log_handler.info("If you have questions for us, "
                             "please provide us with the get_org.log.txt file "
                             "and the post-slimming graph in the format you like!")
            # log.info("-------------------------------------------------------")
        if not export_succeeded:
            if slim_out_csv:
                log_handler.info(
                    "Please visualize " + slim_out_fg + " and load " +
                    slim_out_csv + " to confirm the incomplete result.")
            # log.info("-------------------------------------------------------")
            log_handler.info("If you have questions for us, "
                             "please provide us with the get_org.log.txt file "
                             "and the post-slimming graph in the format you like!")
    return export_succeeded


def main():
    time0 = time.time()
    from GetOrganelleLib.versions import get_versions
    title = "GetOrganelle v" + str(get_versions()) + \
            "\n" \
            "\nget_organelle_from_assembly.py isolates organelle genomes from assembly graph." \
            "\nFind updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information." \
            "\n"
    options, log_handler = get_options(description=title, version=get_versions())
    from GetOrganelleLib.assembly_parser import Assembly
    try:
        if executable(os.path.join(UTILITY_PATH, "slim_graph.py -h")):
            which_slim = UTILITY_PATH
        elif executable(os.path.join(PATH_OF_THIS_SCRIPT, "slim_graph.py -h")):
            which_slim = PATH_OF_THIS_SCRIPT
        elif executable("slim_graph.py -h"):
            which_slim = ""
        else:
            raise Exception("slim_graph.py not found!")
        log_handler.info("Processing assembly graph ...")
        if os.path.getsize(options.input_graph) == 0:
            raise Exception("No contigs found in " + options.input_graph + "!")

        in_postfix = ""
        if options.input_graph.lower().endswith(".gfa"):
            in_postfix = "gfa"
        elif options.input_graph.lower().endswith(".fastg"):
            in_postfix = "fastg"
        else:
            raise Exception("Input assembly graph file must have name suffix '.gfa' or '.fastg'.")
        processed_graph_file = os.path.join(options.output_base, options.prefix + "initial_assembly_graph." + in_postfix)
        if options.max_depth != inf or options.min_depth != 0.:
            this_graph = Assembly(
                options.input_graph, max_cov=options.max_depth, min_cov=options.min_depth, log_handler=log_handler)
            if in_postfix.endswith("gfa"):
                this_graph.write_to_gfa(out_file=processed_graph_file, check_postfix=False)
            else:
                this_graph.write_to_fastg(
                    out_file=processed_graph_file, check_postfix=False, rename_if_needed=True,
                    out_renaming_table=os.path.join(
                        options.output_base, options.prefix + "initial_assembly_graph.vertex_trans.tab"),
                    echo_rename_warning=True, log_handler=log_handler)
        else:
            copyfile(options.input_graph, processed_graph_file)
        log_handler.info("Processing assembly graph finished.\n")

        if options.no_slim:
            slimmed_graph_file = processed_graph_file
            slimmed_csv_file = None
        else:
            if os.path.getsize(processed_graph_file) == 0:
                raise Exception("No contigs left in " + processed_graph_file + "! Please adjust the depth range!")
            log_handler.info("Slimming assembly graph ...")
            slimmed_graph_file_base = os.path.join(
                options.output_base, options.prefix + "slimmed_assembly_graph")
            slimmed_graph_file = os.path.join(
                options.output_base, options.prefix + "slimmed_assembly_graph." + in_postfix)
            slimmed_csv_file = os.path.join(
                options.output_base, options.prefix + "slimmed_assembly_graph.csv")
            run_stat = slim_assembly_graph(organelle_types=options.organelle_type, in_custom=options.genes_fasta,
                                           ex_custom=options.exclude_genes, graph_in=processed_graph_file,
                                           graph_out_base=slimmed_graph_file_base,
                                           max_slim_extending_len=options.max_slim_extending_len,
                                           verbose_log=options.verbose_log,
                                           log_handler=log_handler, threads=options.threads,
                                           which_blast=options.which_blast,
                                           which_slim=which_slim, other_options=options.slim_options,
                                           resume=options.script_resume, keep_temp=options.keep_temp_files)
            if run_stat:
                log_handler.error(run_stat + "\n")
                exit()
            else:
                if os.path.getsize(slimmed_graph_file) == 0:
                    raise Exception(
                        "Slimming " + processed_graph_file + " finished with no target organelle contigs found!")
                log_handler.info("Slimming assembly graph finished.\n")

        organelle_type_prefix = []
        duplicated_o_types = {o_type: 1
                              for o_type in options.organelle_type if options.organelle_type.count(o_type) > 1}
        for here_type in options.organelle_type:
            if here_type in duplicated_o_types:
                organelle_type_prefix.append(here_type + "-" + str(duplicated_o_types[here_type]))
                duplicated_o_types[here_type] += 1
            else:
                organelle_type_prefix.append(here_type)
        for go_t, sub_organelle_type in enumerate(options.organelle_type):
            og_prefix = options.prefix + organelle_type_prefix[go_t]
            graph_existed = bool([gfa_f for gfa_f in os.listdir(options.output_base)
                                  if gfa_f.startswith(og_prefix) and gfa_f.endswith(".path_sequence.gfa")])
            fasta_existed = bool([fas_f for fas_f in os.listdir(options.output_base)
                                  if fas_f.startswith(og_prefix) and fas_f.endswith(".path_sequence.fasta")])
            if options.script_resume and graph_existed and fasta_existed:
                log_handler.info("Extracting " + sub_organelle_type + " from the assemblies ... skipped.\n")
            else:
                # log_handler.info("Parsing assembly graph and outputting ...")
                log_handler.info("Extracting " + sub_organelle_type + " from the assemblies ...")
                if options.genes_fasta:
                    db_base_name = remove_db_postfix(os.path.basename(options.genes_fasta[go_t]))
                else:
                    db_base_name = sub_organelle_type
                ext_res = extract_organelle_genome(out_base=options.output_base,
                                                   slim_out_fg=slimmed_graph_file, slim_out_csv=slimmed_csv_file,
                                                   organelle_prefix=og_prefix,
                                                   organelle_type=sub_organelle_type,
                                                   blast_db=db_base_name,
                                                   verbose=options.verbose_log, log_handler=log_handler,
                                                   expected_minimum_size=options.expected_min_size[go_t],
                                                   expected_maximum_size=options.expected_max_size[go_t],
                                                   no_slim=options.no_slim, options=options)
                if ext_res:
                    log_handler.info("Extracting " + sub_organelle_type + " from the assemblies finished.\n")
                else:
                    log_handler.info("Extracting " + sub_organelle_type + " from the assemblies failed.\n")
        log_handler = simple_log(log_handler, options.output_base, prefix=options.prefix + "get_org.")
        log_handler.info("\nTotal cost " + "%.2f" % (time.time() - time0) + " s")
        log_handler.info("Thank you!")
    except:
        log_handler.exception("")
        final_error_summary_log(log_handler, options.output_base, options.prefix, time0, "the slimmed_assembly_graph.*")
    logging.shutdown()


if __name__ == '__main__':
    main()


"""Copyright 2016 Jianjun Jin

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License."""