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get_organelle_from_assembly.py
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#!/usr/bin/env python
try:
from math import inf
except ImportError:
inf = float("inf")
from optparse import OptionParser
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 shutil import copyfile
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))
LBL_DB_PATH = os.path.realpath(os.path.join(GO_LIB_PATH, "LabelDatabase"))
SEQ_DB_PATH = os.path.realpath(os.path.join(GO_LIB_PATH, "SeedDatabase"))
UTILITY_PATH = os.path.join(PATH_OF_THIS_SCRIPT, "Utilities")
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 = OptionParser(usage=usage, version=version, description=description, add_help_option=False)
parser.add_option("-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), "
"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, with customized gene database "
"('--genes'), which is suggested only when the above database is genetically distant "
"from your sample) or raw (disentangle the raw graph directly without tagging).")
parser.add_option("-g", dest="input_graph", help="Input assembly graph (fastg/gfa) file. "
"The format will be recognized by the file name suffix.")
parser.add_option("-o", dest="output_base", help="Output directory. Overwriting files if directory exists.")
parser.add_option('--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.')
parser.add_option('--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.')
parser.add_option("--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_option("--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_option("--no-slim", dest="no_slim", default=False, action="store_true",
help="Disable slimming process and directly disentangle the original assembly graph. "
"Default: %default")
parser.add_option("--slim-options", dest="slim_options", default="",
help="Other options for calling slim_graph.py")
parser.add_option("--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/animal_mt), "
"maximum_of_type1_type2 (-F type1,type2), inf (-F anonym)")
parser.add_option("--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_option("--depth-factor", dest="depth_factor", default=10.0, type=float,
help="Depth factor for differentiate genome type of contigs. "
"The genome type of contigs are determined by blast. "
"Default: %default")
parser.add_option("--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")
parser.add_option("--contamination-depth", dest="contamination_depth", default=3., type=float,
help="Depth factor for confirming contamination in parallel contigs. Default: %default")
parser.add_option("--contamination-similarity", dest="contamination_similarity", default=0.9, type=float,
help="Similarity threshold for confirming contaminating contigs. Default: %default")
parser.add_option("--no-degenerate", dest="degenerate", default=True, action="store_false",
help="Disable making consensus from parallel contig based on nucleotide degenerate table.")
parser.add_option("--degenerate-depth", dest="degenerate_depth", default=1.5, type=float,
help="Depth factor for confirming parallel contigs. Default: %default")
parser.add_option("--degenerate-similarity", dest="degenerate_similarity", default=0.98, type=float,
help="Similarity threshold for confirming parallel contigs. Default: %default")
parser.add_option("--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")
parser.add_option("--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/animal_mt), "
"1000000 (-F embplant_mt/other_pt), "
"1000000,1000000,250000 (-F other_pt,embplant_mt,fungus_mt)")
parser.add_option("--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 for all.")
parser.add_option("--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_option("--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")
parser.add_option("--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_option("--min-sigma", dest="min_sigma_factor", type=float, default=0.1,
help="Minimum deviation factor for excluding non-target contigs. Default:%default")
parser.add_option("--max-multiplicity", dest="max_multiplicity", type=int, default=8,
help="Maximum multiplicity of contigs for disentangling genome paths. "
"Should be 1~12. Default:%default")
parser.add_option("-t", dest="threads", type=int, default=1,
help="Maximum threads to use.")
parser.add_option("--prefix", dest="prefix", default="",
help="Add extra prefix to resulting files under the output directory.")
parser.add_option("--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("GetOrganelleDep") + "/" + SYSTEM_NAME +
"/ncbi-blast\" first, then $PATH")
parser.add_option("--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_option("--keep-temp", dest="keep_temp_files", action="store_true", default=False,
help="Choose to keep the running temp/index files.")
parser.add_option("--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_option("--random-seed", dest="random_seed", default=12345, type=int,
help="Default: %default")
parser.add_option("--verbose", dest="verbose_log", action="store_true", default=False,
help="Verbose output. Choose to enable verbose running log_handler.")
parser.add_option("-h", dest="simple_help", default=False, action="store_true",
help="print brief introduction for frequently-used options.")
parser.add_option("--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()
elif "-h" in sys.argv:
for not_often_used in ("--genes", "--ex-genes", "--slim-options", "--max-slim-extending-len",
"--depth-factor", "--spades-out-dir", "--type-f",
"--contamination-depth", "--contamination-similarity", "--no-degenerate",
"--degenerate-depth", "--degenerate-similarity", "--disentangle-time-limit",
"--expected-max-size", "--expected-min-size", "--reverse-lsc", "--max-paths-num",
"--keep-all-polymorphic", "--min-sigma", "--max-multiplicity",
"--prefix", "--which-blast", "--which-bandage",
"--keep-temp", "--random-seed", "--verbose"):
parser.remove_option(not_often_used)
parser.remove_option("-F")
parser.add_option("-F", dest="organelle_type",
help="Target organelle genome type(s): "
"embplant_pt/other_pt/embplant_mt/embplant_nr/animal_mt/fungus_mt/anonym/"
"embplant_pt,embplant_mt/other_pt,embplant_mt,fungus_mt")
parser.remove_option("-g")
parser.add_option("-g", dest="input_graph", help="Input assembly graph (fastg/gfa) file.")
parser.remove_option("-o")
parser.add_option("-o", dest="output_base", help="Output directory.")
parser.remove_option("--min-depth")
parser.add_option("--min-depth", dest="min_depth", default=0., type=float,
help="Minimum depth threshold of contigs. Default: %default.")
parser.remove_option("--max-depth")
parser.add_option("--max-depth", dest="max_depth", default=inf, type=float,
help="Maximum depth threshold of contigs. Default: %default.")
parser.remove_option("--no-slim")
parser.add_option("--no-slim", dest="no_slim",
help="Disable the slimming process and directly disentangle the assembly graph.")
parser.remove_option("-t")
parser.add_option("-t", dest="threads", type=int, default=1, help="Maximum threads to use. Default: %default.")
parser.remove_option("--continue")
parser.add_option("--continue", dest="script_resume", default=False, action="store_true",
help="Resume a previous run. Default: %default.")
parser.print_help()
sys.stdout.write("\n")
exit()
else:
pass
# 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, args) = parser.parse_args()
except Exception as e:
sys.stdout.write("\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(",")
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"
"\nInstall it 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", "anonym"}:
sys.stdout.write("\n############################################################################"
"\nERROR: \"-F\" MUST be one of 'embplant_pt', 'other_pt', 'embplant_mt', "
"'embplant_nr', 'animal_mt', 'fungus_mt', '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
organelle_type_len = len(options.organelle_type)
options.prefix = os.path.basename(options.prefix)
if not os.path.isdir(options.output_base):
os.mkdir(options.output_base)
options.script_resume = False
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 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 scipy
except ImportError:
log_handler.error("scipy is not available! Please install scipy!")
sys.exit()
else:
lib_versions_info.append("scipy " + scipy.__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))
# existing default database
if not options.no_slim:
existing_seed_db, existing_label_db = get_current_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")
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", "animal_mt"):
options.expected_max_size.append(int(raw_default_value / 10))
elif sub_organelle_t == "anonym":
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:
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)
try:
import numpy as np
except ImportError:
pass
else:
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 + ".fastg") 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").lower():
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
def disentangle_assembly(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(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_copy_in=10, 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:
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:
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(
broken_graph_allowed=acyclic_allowed_in, return_new_graphs=True, verbose=verbose_in,
log_handler=log_in)
else:
target_results = input_graph.find_target_graph(tab_f,
mode=mode_in, database_name=in_db_n, type_factor=type_f,
log_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,
max_contig_multiplicity=max_copy_in,
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)
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
these_paths = broken_graph.get_all_paths(mode=mode_in, log_handler=log_in)
# reducing paths
if len(these_paths) > options.max_paths_num:
log_in.warning("Only exporting " + str(options.max_paths_num) + " out of all " +
str(len(these_paths)) + " 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) + ".selected_graph."
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) + ".selected_graph."
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) + ".selected_graph."
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
these_paths = idealized_graph.get_all_circular_paths(
mode=mode_in, log_handler=log_in, reverse_start_direction_for_pt=options.reverse_lsc)
# reducing paths
if len(these_paths) > options.max_paths_num:
log_in.warning("Only exporting " + str(options.max_paths_num) + " out of all " +
str(len(these_paths)) + " 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) + ".selected_graph."
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(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_copy_in=here_max_copy, max_cov_in=here_only_max_c,
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)
# start
timeout_flag = "'--disentangle-time-limit'"
export_succeeded = False
path_prefix = os.path.join(out_base, organelle_prefix)
graph_temp_file = path_prefix + ".temp.gfa" if options.keep_temp_files else None
try:
"""disentangle"""
disentangle_assembly(fastg_file=slim_out_fg, blast_db_base=blast_db, mode=organelle_type,
tab_file=slim_out_csv, output=path_prefix,
weight_factor=100, 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_file)
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 failed: 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 failed: " + str(e).strip())
except Exception as e:
log_handler.exception("")
raise e
else:
export_succeeded = True
if not export_succeeded:
try:
"""disentangle"""
disentangle_assembly(fastg_file=slim_out_fg, blast_db_base=blast_db, mode=organelle_type,
tab_file=slim_out_csv, output=path_prefix,
weight_factor=100, 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_file)
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 failed: 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 failed: " + str(e).strip())
except Exception as e:
log_handler.exception("")
raise e
else:
export_succeeded = True
if not export_succeeded:
try:
"""disentangle the graph as scaffold(s)/contig(s)"""
disentangle_assembly(fastg_file=slim_out_fg, blast_db_base=blast_db, mode=organelle_type,
tab_file=slim_out_csv, output=path_prefix,
weight_factor=100, type_factor=options.type_factor,
here_verbose=verbose, log_dis=log_handler,
hard_cov_threshold=options.depth_factor * 0.8,
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_file)
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 failed: 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 failed: " + 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")):
which_slim = UTILITY_PATH
elif executable(os.path.join(PATH_OF_THIS_SCRIPT, "slim_graph.py")):
which_slim = PATH_OF_THIS_SCRIPT
elif executable("slim_graph.py"):
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)
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:
return "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)