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get_organelle_from_reads.py
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get_organelle_from_reads.py
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#!/usr/bin/env python
import datetime
import shutil
from copy import deepcopy
from math import log, exp
try:
from math import inf
except ImportError:
inf = float("inf")
from argparse import ArgumentParser
import GetOrganelleLib
from GetOrganelleLib.seq_parser import *
from GetOrganelleLib.pipe_control_func import *
import time
import random
import subprocess
import sys
import os
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)
MAX_RATIO_RL_WS = 0.75
AUTO_MIN_WS = 49
AUTO_MIN_WS_ANIMAL_MT = 41
AUTO_MIN_WS_PLANT_MT = 55
GLOBAL_MIN_WS = 29
BASE_COV_SAMPLING_PERCENT = 0.06
GUESSING_FQ_GZIP_COMPRESSING_RATIO = 3.58
GUESSING_FQ_SEQ_INFLATE_TO_FILE = 3.22
SUPPORTED_ORGANELLE_TYPES = ["embplant_pt", "embplant_mt", "embplant_nr", "other_pt", "animal_mt", "fungus_mt", "fungus_nr"]
ORGANELLE_EXPECTED_GRAPH_SIZES = {"embplant_pt": 130000,
"embplant_mt": 390000,
"embplant_nr": 13000,
"fungus_nr": 13000,
"other_pt": 39000,
"animal_mt": 13000,
"fungus_mt": 65000}
READ_LINE_TO_INF = int(HEAD_MAXIMUM_LINES/4)
def get_options(description, version):
version = version
usage = "\n### Embryophyta plant plastome, 2*(1G raw data, 150 bp) reads\n" + str(os.path.basename(__file__)) + \
" -1 sample_1.fq -2 sample_2.fq -s cp_seed.fasta -o plastome_output " \
" -R 15 -k 21,45,65,85,105 -F embplant_pt\n" \
"### Embryophyta plant mitogenome\n" + str(os.path.basename(__file__)) + \
" -1 sample_1.fq -2 sample_2.fq -s mt_seed.fasta -o mitogenome_output " \
" -R 30 -k 21,45,65,85,105 -F embplant_mt"
parser = ArgumentParser(usage=usage, description=description, add_help=False)
# simple help mode
if "-h" in sys.argv:
parser.add_argument("-1", dest="fq_file_1", help="Input file with forward paired-end reads (*.fq/.gz/.tar.gz).")
parser.add_argument("-2", dest="fq_file_2", help="Input file with reverse paired-end reads (*.fq/.gz/.tar.gz).")
parser.add_argument("-u", dest="unpaired_fq_files", help="Input file(s) with unpaired (single-end) reads. ")
parser.add_argument("-o", dest="output_base", help="Output directory.")
parser.add_argument("-s", dest="seed_file", help="Input fasta format file as initial seed. "
"Default: " + os.path.join(SEQ_DB_PATH, "*.fasta"))
parser.add_argument("-w", dest="word_size", help="Word size (W) for extension. Default: auto-estimated")
parser.add_argument("-R", dest="max_rounds", help="Maximum extension rounds (suggested: >=2). "
"Default: 15 (embplant_pt)")
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("--max-reads", type=float,
help="Maximum number of reads to be used per file. "
"Default: 1.5E7 (-F embplant_pt/embplant_nr/fungus_mt/fungus_nr); "
"7.5E7 (-F embplant_mt/other_pt/anonym); 3E8 (-F animal_mt)")
parser.add_argument("--fast", dest="fast_strategy",
help="=\"-R 10 -t 4 -J 5 -M 7 --max-n-words 3E7 --larger-auto-ws "
"--disentangle-time-limit 360\"")
parser.add_argument("-k", dest="spades_kmer", default="21,55,85,115",
help="SPAdes kmer settings. Default: %(default)s")
parser.add_argument("-t", dest="threads", type=int, default=1,
help="Maximum threads to use. Default: %(default)s")
parser.add_argument("-P", dest="pre_grouped", default=int(2E5), help="Pre-grouping value. Default: %(default)s")
parser.add_argument("-v", "--version", action="version",
version="GetOrganelle v{version}".format(version=version))
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.")
parser.print_help()
sys.stdout.write("\n")
exit()
else:
# verbose help mode
# group 1
group_inout = parser.add_argument_group("IN-OUT OPTIONS", "Options on inputs and outputs")
# group_inout = OptionGroup(parser, "IN-OUT OPTIONS", "Options on inputs and outputs")
group_inout.add_argument("-1", dest="fq_file_1",
help="Input file with forward paired-end reads (format: fastq/fastq.gz/fastq.tar.gz).")
group_inout.add_argument("-2", dest="fq_file_2",
help="Input file with reverse paired-end reads (format: fastq/fastq.gz/fastq.tar.gz).")
group_inout.add_argument("-u", dest="unpaired_fq_files",
help="Input file(s) with unpaired (single-end) reads (format: fastq/fastq.gz/fastq.tar.gz). "
"files could be comma-separated lists such as 'seq1.fq,seq2.fq'.")
group_inout.add_argument("-o", dest="output_base",
help="Output directory. Overwriting files if directory exists.")
group_inout.add_argument("-s", dest="seed_file", default=None,
help="Seed sequence(s). Input fasta format file as initial seed. "
"A seed sequence in GetOrganelle is only used for identifying initial "
"organelle reads. The assembly process is purely de novo. "
"Should be a list of files split by comma(s) on a multi-organelle mode, "
"with the same list length to organelle_type (followed by '-F'). "
"Default: '" + os.path.join(SEQ_DB_PATH, "*.fasta") + "' "
"(* depends on the value followed with flag '-F')")
group_inout.add_argument("-a", dest="anti_seed",
help="Anti-seed(s). Not suggested unless what you really know what you are doing. "
"Input fasta format file as anti-seed, where the extension process "
"stop. Typically serves as excluding plastid reads when extending mitochondrial "
"reads, or the other way around. You should be cautious about using this option, "
"because if the anti-seed includes some word in the target but not in the seed, "
"the result would have gaps. For example, use the embplant_mt and embplant_pt "
"from the same plant-species as seed and anti-seed.")
group_inout.add_argument("--max-reads", dest="maximum_n_reads", type=float, default=1.5E7,
help="Hard bound for maximum number of reads to be used per file. "
"A input larger than " + str(
READ_LINE_TO_INF) + " will be treated as infinity (INF). "
"Default: 1.5E7 (-F embplant_pt/embplant_nr/fungus_mt/fungus_nr); "
"7.5E7 (-F embplant_mt/other_pt/anonym); 3E8 (-F animal_mt)")
group_inout.add_argument("--reduce-reads-for-coverage", dest="reduce_reads_for_cov", type=float, default=500,
help="Soft bound for maximum number of reads to be used according to "
"target-hitting base coverage. "
"If the estimated target-hitting base coverage is too high and "
"over this VALUE, GetOrganelle automatically reduce the number of reads to "
"generate a final assembly with base coverage close to this VALUE. "
"This design could greatly save computational resources in many situations. "
"A mean base coverage over 500 is extremely sufficient for most cases. "
"This VALUE must be larger than 10. Set this VALUE to inf to disable reducing. "
"Default: %(default)s.")
group_inout.add_argument("--max-ignore-percent", dest="maximum_ignore_percent", type=float, default=0.01,
help="The maximum percent of bases to be ignore in extension, due to low quality. "
"Default: %(default)s")
group_inout.add_argument("--phred-offset", dest="phred_offset", default=-1, type=int,
help="Phred offset for spades-hammer. Default: GetOrganelle-autodetect")
group_inout.add_argument("--min-quality-score", dest="min_quality_score", type=int, default=1,
help="Minimum quality score in extension. This value would be automatically decreased "
"to prevent ignoring too much raw data (see --max-ignore-percent)."
"Default: %(default)s ('\"' in Phred+33; 'A' in Phred+64/Solexa+64)")
group_inout.add_argument("--prefix", dest="prefix", default="",
help="Add extra prefix to resulting files under the output directory.")
group_inout.add_argument("--out-per-round", dest="fg_out_per_round", action="store_true", default=False,
help="Enable output per round. Choose to save memory but cost more time per round.")
group_inout.add_argument("--zip-files", dest="zip_files", action="store_true", default=False,
help="Choose to compress fq/sam files using gzip.")
group_inout.add_argument("--keep-temp", dest="keep_temp_files", action="store_true", default=False,
help="Choose to keep the running temp/index files.")
group_inout.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)
# group 2
group_scheme = parser.add_argument_group("SCHEME OPTIONS", "Options on running schemes.")
group_scheme.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 mitogenome), embplant_nr (plant nuclear ribosomal RNA), animal_mt "
"(animal mitogenome), fungus_mt (fungus mitogenome), "
"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'). "
"For easy usage and compatibility of old versions, following redirection "
"would be automatically fulfilled without warning:\t"
"\nplant_cp->embplant_pt; plant_pt->embplant_pt; "
"\nplant_mt->embplant_mt; plant_nr->embplant_nr")
group_scheme.add_argument("--fast", dest="fast_strategy", default=False, action="store_true",
help="=\"-R 10 -t 4 -J 5 -M 7 --max-n-words 3E7 --larger-auto-ws "
"--disentangle-time-limit 360\" "
"This option is suggested for homogeneously and highly covered data (very fine data). "
"You can overwrite the value of a specific option listed above by adding "
"that option along with the \"--fast\" flag. "
"You could try GetOrganelle with this option for a list of samples and run a second "
"time without this option for the rest with incomplete results. ")
group_scheme.add_argument("--memory-save", dest="memory_save", default=False, action="store_true",
help="=\"--out-per-round -P 0 --remove-duplicates 0\" "
"You can overwrite the value of a specific option listed above by adding "
"that option along with the \"--memory-save\" flag. A larger '-R' value is suggested "
"when \"--memory-save\" is chosen.")
group_scheme.add_argument("--memory-unlimited", dest="memory_unlimited", default=False, action="store_true",
help="=\"-P 1E7 --index-in-memory --remove-duplicates 2E8 "
"--min-quality-score -5 --max-ignore-percent 0\" "
"You can overwrite the value of a specific option listed above by adding "
"that option along with the \"--memory-unlimited\" flag. ")
# group 3
group_extending = parser.add_argument_group("EXTENDING OPTIONS",
"Options on the performance of extending process")
group_extending.add_argument("-w", dest="word_size", type=float,
help="Word size (W) for pre-grouping (if not assigned by '--pre-w') and extending "
"process. This script would try to guess (auto-estimate) a proper W "
"using an empirical function based on average read length, reads quality, "
"target genome coverage, and other variables that might influence the extending "
"process. You could assign the ratio (1>input>0) of W to "
"read_length, based on which this script would estimate the W for you; "
"or assign an absolute W value (read length>input>=35). Default: auto-estimated.")
group_extending.add_argument("--pre-w", dest="pregroup_word_size", type=float,
help="Word size (W) for pre-grouping. Used to reproduce result when word size is "
"a certain value during pregrouping process and later changed during reads "
"extending process. Similar to word size. Default: the same to word size.")
group_extending.add_argument("-R", "--max-rounds", dest="max_rounds", type=int, # default=inf,
help="Maximum number of extending rounds (suggested: >=2). "
"Default: 15 (-F embplant_pt), 30 (-F embplant_mt/other_pt), "
"10 (-F embplant_nr/animal_mt/fungus_mt/fungus_nr), inf (-P 0).")
group_extending.add_argument("--max-n-words", dest="maximum_n_words", type=float, default=4E8,
help="Maximum number of words to be used in total."
"Default: 4E8 (-F embplant_pt), 2E8 (-F embplant_nr/fungus_mt/fungus_nr/animal_mt), "
"2E9 (-F embplant_mt/other_pt)")
group_extending.add_argument("-J", dest="jump_step", type=int, default=3,
help="The length of step for checking words in reads during extending process "
"(integer >= 1). When you have reads of high quality, the larger the number is, "
"the faster the extension will be, "
"the more risk of missing reads in low coverage area. "
"Choose 1 to choose the slowest but safest extension strategy. Default: %(default)s")
group_extending.add_argument("-M", dest="mesh_size", type=int, default=2,
help="(Beta parameter) "
"The length of step for building words from seeds during extending process "
"(integer >= 1). When you have reads of high quality, the larger the number is, "
"the faster the extension will be, "
"the more risk of missing reads in low coverage area. "
"Another usage of this mesh size is to choose a larger mesh size coupled with a "
"smaller word size, which makes smaller word size feasible when memory is limited."
"Choose 1 to choose the slowest but safest extension strategy. Default: %(default)s")
group_extending.add_argument("--bowtie2-options", dest="bowtie2_options", default="--very-fast -t",
help="Bowtie2 options, such as '--ma 3 --mp 5,2 --very-fast -t'. Default: %(default)s.")
group_extending.add_argument("--larger-auto-ws", dest="larger_auto_ws", default=False, action="store_true",
help="By using this flag, the empirical function for estimating W would tend to "
"produce a relative larger W, which would speed up the matching in extending, "
"reduce the memory cost in extending, but increase the risk of broken final "
"graph. Suggested when the data is good with high and homogenous coverage.")
mixed_organelles = ("other_pt", "embplant_mt", "fungus_mt")
group_extending.add_argument("--target-genome-size", dest="target_genome_size", default='130000', type=str,
help="Hypothetical value(s) of target genome size. This is only used for estimating "
"word size when no '-w word_size' is given. "
"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: " +
" or ".join(
[str(
ORGANELLE_EXPECTED_GRAPH_SIZES[this_type]) + " (-F " + this_type + ")"
for this_type in SUPPORTED_ORGANELLE_TYPES]) + " or " +
",".join([str(ORGANELLE_EXPECTED_GRAPH_SIZES[this_type])
for this_type in mixed_organelles]) +
" (-F " + ",".join(mixed_organelles) + ")")
group_extending.add_argument("--max-extending-len", dest="max_extending_len", type=str,
help="Maximum extending length(s) derived from the seed(s). "
"A single value could be a non-negative number, or inf (infinite) "
"or auto (automatic estimation). "
"This is designed for properly stopping the extending from getting too long and "
"saving computational resources. However, empirically, a maximum extending length "
"value larger than 6000 would not be helpful for saving computational resources. "
"This value would not be precise in controlling output size, especially "
"when pre-group (followed by '-P') is turn on."
"In the auto mode, the maximum extending length is estimated based on the sizes of "
"the gap regions that not covered in the seed sequences. A sequence of a closely "
"related species would be preferred for estimating a better maximum extending "
"length value. If you are using limited loci, e.g. rbcL gene as the seed for "
"assembling the whole plastome (with extending length ca. 75000 >> 6000), "
"you should set maximum extending length to inf. "
"Should be a list of numbers/auto/inf split by comma(s) on a multi-organelle mode, "
"with the same list length to organelle_type (followed by '-F'). "
"Default: inf. ")
# group 4
group_assembly = parser.add_argument_group("ASSEMBLY OPTIONS", "These options are about the assembly and "
"graph disentangling")
group_assembly.add_argument("-k", dest="spades_kmer", default="21,55,85,115",
help="SPAdes kmer settings. Use the same format as in SPAdes. illegal kmer values "
"would be automatically discarded by GetOrganelle. "
"Default: %(default)s")
group_assembly.add_argument("--spades-options", dest="other_spades_options", default="",
help="Other SPAdes options. Use double quotation marks to include all "
"the arguments and parameters.")
group_assembly.add_argument("--no-spades", dest="run_spades", action="store_false", default=True,
help="Disable SPAdes.")
group_assembly.add_argument("--ignore-k", dest="ignore_kmer_res", default=40, type=int,
help="A kmer threshold below which, no slimming/disentangling would be executed"
" on the result. Default: %(default)s")
group_assembly.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 become invalid when '--genes' or '--ex-genes' is used.")
group_assembly.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 will become invalid when '--genes' or '--ex-genes' is used.")
group_assembly.add_argument("--disentangle-df", dest="disentangle_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)s")
group_assembly.add_argument("--contamination-depth", dest="contamination_depth", default=3., type=float,
help="Depth factor for confirming contamination in parallel contigs. Default: %(default)s")
group_assembly.add_argument("--contamination-similarity", dest="contamination_similarity", default=0.9,
type=float,
help="Similarity threshold for confirming contaminating contigs. Default: %(default)s")
group_assembly.add_argument("--no-degenerate", dest="degenerate", default=True, action="store_false",
help="Disable making consensus from parallel contig based on nucleotide degenerate table.")
group_assembly.add_argument("--degenerate-depth", dest="degenerate_depth", default=1.5, type=float,
help="Depth factor for confirming parallel contigs. Default: %(default)s")
group_assembly.add_argument("--degenerate-similarity", dest="degenerate_similarity", default=0.98, type=float,
help="Similarity threshold for confirming parallel contigs. Default: %(default)s")
group_assembly.add_argument("--disentangle-time-limit", dest="disentangle_time_limit", default=1800, 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")
group_assembly.add_argument("--expected-max-size", dest="expected_max_size", default='250000', 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/fungus_nr), 1000000 (-F embplant_mt/other_pt),"
"1000000,1000000,250000 (-F other_pt,embplant_mt,fungus_mt)")
group_assembly.add_argument("--expected-min-size", dest="expected_min_size", default=10000, type=str,
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.")
group_assembly.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 region) 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.")
group_assembly.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")
# group 5
group_computational = parser.add_argument_group("ADDITIONAL OPTIONS", "")
group_computational.add_argument("-t", dest="threads", type=int, default=1,
help="Maximum threads to use.")
group_computational.add_argument("-P", dest="pre_grouped", type=float, default=2E5,
help="The maximum number (integer) of high-covered reads to be pre-grouped "
"before extending process. pre_grouping is suggested when the whole genome "
"coverage is shallow but the organ genome coverage is deep. "
"The default value is 2E5. "
"For personal computer with 8G memory, we suggest no more than 3E5. "
"A larger number (ex. 6E5) would run faster but exhaust memory "
"in the first few minutes. Choose 0 to disable this process.")
group_computational.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")
group_computational.add_argument("--which-bowtie2", dest="which_bowtie2", default="",
help="Assign the path to Bowtie2 binary files if not added to the path. "
"Default: try \"" + os.path.realpath(GO_DEP_PATH) +
"/bowtie2\" first, then $PATH")
group_computational.add_argument("--which-spades", dest="which_spades", default="",
help="Assign the path to SPAdes binary files if not added to the path. "
"Default: try \"" + os.path.realpath(GO_DEP_PATH) +
"/SPAdes\" first, then $PATH")
group_computational.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")
group_computational.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.")
group_computational.add_argument("--overwrite", dest="script_overwrite", default=False, action="store_true",
help="Overwrite previous file if existed. ")
group_computational.add_argument("--index-in-memory", dest="index_in_memory", action="store_true",
default=False,
help="Keep index in memory. Choose save index in memory than in disk.")
group_computational.add_argument("--remove-duplicates", dest="rm_duplicates", default=1E7, type=float,
help="By default this script use unique reads to extend. Choose the number of "
"duplicates (integer) to be saved in memory. A larger number (ex. 2E7) would "
"run faster but exhaust memory in the first few minutes. "
"Choose 0 to disable this process. "
"Note that whether choose or not will not disable "
"the calling of replicate reads. Default: %(default)s.")
group_computational.add_argument("--flush-step", dest="echo_step", default=54321,
help="Flush step (INTEGER OR INF) for presenting progress. "
"For running in the background, you could set this to inf, "
"which would disable this. Default: %(default)s")
group_computational.add_argument("--random-seed", dest="random_seed", default=12345, type=int,
help="Default: %(default)s")
group_computational.add_argument("--verbose", dest="verbose_log", action="store_true", default=False,
help="Verbose output. Choose to enable verbose running log_handler.")
parser.add_argument("-v", "--version", action="version",
version="GetOrganelle v{version}".format(version=version))
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()
# if "--help" in sys.argv:
# parser.add_option_group(group_inout)
# parser.add_option_group(group_scheme)
# parser.add_option_group(group_extending)
# parser.add_option_group(group_assembly)
# parser.add_option_group(group_computational)
#
# elif "-h" in sys.argv:
# for not_often_used in ("-a", "--max-ignore-percent", "--reduce-reads-for-coverage", "--phred-offset",
# "--min-quality-score", "--prefix", "--out-per-round", "--zip-files", "--keep-temp",
# "--config-dir",
# "--memory-save", "--memory-unlimited", "--pre-w", "--max-n-words",
# "-J", "-M", "--bowtie2-options",
# "--larger-auto-ws", "--target-genome-size", "--spades-options", "--no-spades",
# "--ignore-k", "--genes", "--ex-genes", "--disentangle-df",
# "--contamination-depth", "--contamination-similarity", "--no-degenerate",
# "--degenerate-depth", "--degenerate-similarity", "--disentangle-time-limit",
# "--expected-max-size", "--expected-min-size", "--reverse-lsc", "--max-paths-num",
# "--which-blast", "--which-bowtie2", "--which-spades", "--which-bandage",
# "--continue", "--overwrite", "--index-in-memory",
# "--remove-duplicates", "--flush-step", "--verbose"):
# parser.remove_option(not_often_used)
#
# else:
# parser.add_option_group(group_inout)
# parser.add_option_group(group_scheme)
# parser.add_option_group(group_extending)
# parser.add_option_group(group_assembly)
# parser.add_option_group(group_computational)
# 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.stderr.write("\n############################################################################\n" + str(e))
sys.stderr.write("\n\"-h\" for more usage\n")
exit()
else:
# if pos_args:
# sys.stderr.write("\n############################################################################"
# "\nUnrecognized options: " + "\", \"".join(pos_args) + "\n")
# exit()
if not ((options.fq_file_1 and options.fq_file_2) or options.unpaired_fq_files):
sys.stderr.write("\n############################################################################"
"\nERROR: Insufficient arguments!\n")
sys.stderr.write("Missing/Illegal input reads file(s) (followed after '-1&-2' and/or '-u')!\n")
exit()
if not options.output_base:
sys.stderr.write("\n############################################################################"
"\nERROR: Insufficient arguments!\n")
sys.stderr.write("Missing option: output directory (followed after '-o')!\n")
exit()
if not options.organelle_type:
sys.stderr.write("\n############################################################################"
"\nERROR: Insufficient arguments!\n")
sys.stderr.write("Missing option: organelle type (followed after '-F')!\n")
exit()
else:
options.organelle_type = options.organelle_type.split(",")
if int(bool(options.fq_file_1)) + int(bool(options.fq_file_2)) == 1:
sys.stderr.write("\n############################################################################"
"\nERROR: unbalanced paired reads!\n\n")
exit()
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.stderr.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)
and
(os.path.isfile(os.path.join(_SEQ_DB_PATH, this_sub_organelle + ".fasta")) or options.seed_file)):
sys.stderr.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", "fungus_nr", "anonym"}:
sys.stderr.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.seed_file or not options.genes_fasta:
sys.stderr.write("\n############################################################################"
"\nERROR: \"-s\" and \"--genes\" must be specified 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)
organelle_type_len = len(options.organelle_type)
if not options.seed_file:
use_default_seed = True
options.seed_file = [os.path.join(_SEQ_DB_PATH, sub_o + ".fasta") for sub_o in options.organelle_type]
else:
use_default_seed = False
options.seed_file = str(options.seed_file).split(",")
if len(options.seed_file) != organelle_type_len:
sys.stderr.write("\n############################################################################"
"\nERROR: -F is followed with " + str(organelle_type_len) + " organelle types, " +
"while -s is followed with " + str(len(options.seed_file)) + " file(s)!\n")
exit()
for check_file in [options.fq_file_1, options.fq_file_2, options.anti_seed] + options.seed_file:
if check_file:
if not os.path.exists(check_file):
sys.stderr.write("\n############################################################################"
"\nERROR: " + check_file + " not found!\n\n")
exit()
if os.path.getsize(check_file) == 0:
sys.stderr.write("\n############################################################################"
"\nERROR: " + check_file + " is empty!\n\n")
exit()
if options.unpaired_fq_files:
options.unpaired_fq_files = options.unpaired_fq_files.split(",")
for fastq_file in options.unpaired_fq_files:
if not os.path.exists(fastq_file):
sys.stderr.write("\n############################################################################"
"\nERROR: " + fastq_file + " not found!\n\n")
exit()
else:
options.unpaired_fq_files = []
if options.jump_step < 1:
sys.stderr.write("\n############################################################################"
"\nERROR: Jump step MUST be an integer that >= 1\n")
exit()
if options.mesh_size < 1:
sys.stderr.write("\n############################################################################"
"\nERROR: Mesh size MUST be an integer that >= 1\n")
exit()
if options.fq_file_1 == options.fq_file_2 and options.fq_file_1:
sys.stderr.write("\n############################################################################"
"\nERROR: 1st fastq file is the same with 2nd fastq file!\n")
exit()
if options.memory_save and options.memory_unlimited:
sys.stderr.write("\n############################################################################"
"\nERROR: \"--memory-save\" and \"--memory-unlimited\" are not compatible!\n")
assert options.threads > 0
if options.reduce_reads_for_cov < 10:
sys.stderr.write("\n############################################################################"
"\nERROR: value after \"--reduce-reads-for-coverage\" must be larger than 10!\n")
exit()
if options.echo_step == "inf":
options.echo_step = inf
elif type(options.echo_step) == int:
pass
elif type(options.echo_step) == str:
try:
options.echo_step = int(float(options.echo_step))
except ValueError:
sys.stderr.write("\n############################################################################"
"\n--flush-step should be followed by positive integer or inf!\n")
exit()
assert options.echo_step > 0
assert options.max_paths_num > 0
assert options.phred_offset in (-1, 64, 33)
assert options.script_resume + options.script_overwrite < 2, "'--overwrite' conflicts with '--continue'"
options.prefix = os.path.basename(options.prefix)
if os.path.isdir(options.output_base):
if options.script_resume:
previous_attributes = LogInfo(options.output_base, options.prefix).__dict__
else:
if options.script_overwrite:
try:
shutil.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()
previous_attributes = {}
else:
options.script_resume = False
os.mkdir(options.output_base)
previous_attributes = {}
# if options.script_resume and os.path.isdir(options.output_base):
# previous_attributes = LogInfo(options.output_base, options.prefix).__dict__
# else:
# previous_attributes = {}
# options.script_resume = False
# 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_handler.info("PLATFORM: " + " ".join(platform.uname()))
# log versions of dependencies
lib_versions_info = []
lib_not_available = []
lib_versions_info.append("GetOrganelleLib " + GetOrganelleLib.__version__)
try:
import numpy
except ImportError:
lib_not_available.append("numpy")
else:
lib_versions_info.append("numpy " + numpy.__version__)
try:
import sympy
except ImportError:
lib_not_available.append("sympy")
else:
lib_versions_info.append("sympy " + sympy.__version__)
try:
import scipy
except ImportError:
lib_not_available.append("scipy")
else:
lib_versions_info.append("scipy " + scipy.__version__)
try:
import psutil
except ImportError:
pass
else:
lib_versions_info.append("psutil " + psutil.__version__)
log_handler.info("PYTHON LIBS: " + "; ".join(lib_versions_info))
options.which_bowtie2 = detect_bowtie2_path(options.which_bowtie2, GO_DEP_PATH)
if options.run_spades:
options.which_spades = detect_spades_path(options.which_spades, GO_DEP_PATH)
options.which_blast = detect_blast_path(options.which_blast, GO_DEP_PATH)
dep_versions_info = []
dep_versions_info.append(detect_bowtie2_version(options.which_bowtie2))
if options.run_spades:
dep_versions_info.append(detect_spades_version(options.which_spades))
dep_versions_info.append(detect_blast_version(options.which_blast))
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 database
log_handler.info("GETORG_PATH=" + _GO_PATH)
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)
if use_default_seed:
log_seed_types = deepcopy(options.organelle_type)
if "embplant_pt" in log_seed_types and "embplant_mt" not in log_seed_types:
log_seed_types.append("embplant_mt")
if "embplant_mt" in log_seed_types and "embplant_pt" not in log_seed_types:
log_seed_types.append("embplant_pt")
log_handler.info("SEED DB: " + single_line_db_versions(existing_seed_db, log_seed_types))
if not options.genes_fasta:
log_label_types = deepcopy(options.organelle_type)
if "embplant_pt" in log_label_types and "embplant_mt" not in log_label_types:
log_label_types.append("embplant_mt")
if "embplant_mt" in log_label_types and "embplant_pt" not in log_label_types:
log_label_types.append("embplant_pt")
log_handler.info("LABEL DB: " + single_line_db_versions(existing_label_db, log_label_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")
# if options.run_spades:
# space is forbidden for both spades and blast
for fq_file in [options.fq_file_1, options.fq_file_2] * int(bool(options.fq_file_1 and options.fq_file_2))\
+ options.unpaired_fq_files:
assert is_valid_path(os.path.basename(fq_file)), \
"Invalid characters (e.g. space, non-ascii) for SPAdes in file name: " + os.path.basename(fq_file)
for fq_file in [options.output_base, options.prefix]:
assert is_valid_path(os.path.realpath(fq_file)), \
"Invalid characters (e.g. space, non-ascii) for SPAdes in path: " + os.path.realpath(fq_file)
log_handler = timed_log(log_handler, options.output_base, options.prefix + "get_org.")
if options.word_size is None:
pass
elif 0 < options.word_size < 1:
pass
elif options.word_size >= GLOBAL_MIN_WS:
options.word_size = int(options.word_size)
else:
log_handler.error("Illegal word size (\"-w\") value!")
exit()
if options.pregroup_word_size:
if 0 < options.pregroup_word_size < 1:
pass
elif options.pregroup_word_size >= GLOBAL_MIN_WS:
options.pregroup_word_size = int(options.pregroup_word_size)
else:
log_handler.error("Illegal word size (\"--pre-w\") value!")
exit()
if options.fast_strategy:
if "-R" not in sys.argv and "--max-rounds" not in sys.argv:
options.max_rounds = 10
if "-t" not in sys.argv:
options.threads = 4
if "-J" not in sys.argv:
options.jump_step = 5
if "-M" not in sys.argv:
options.mesh_size = 7
if "--max-n-words" not in sys.argv:
options.maximum_n_words = 3E7
options.larger_auto_ws = True
if "--disentangle-time-limit" not in sys.argv:
options.disentangle_time_limit = 360
if options.memory_save:
if "-P" not in sys.argv:
options.pre_grouped = 0
if "--remove-duplicates" not in sys.argv:
options.rm_duplicates = 0
if options.memory_unlimited:
if "-P" not in sys.argv:
options.pre_grouped = 1E7
if "--remove-duplicates" not in sys.argv:
options.rm_duplicates = 2E8
if "--min-quality-score" not in sys.argv:
options.min_quality_score = -5
if "--max-ignore-percent" not in sys.argv:
options.maximum_ignore_percent = 0
# using the default
if "--max-reads" not in sys.argv:
if "embplant_mt" in options.organelle_type or "anonym" in options.organelle_type:
options.maximum_n_reads *= 5
elif "animal_mt" in options.organelle_type:
options.maximum_n_reads *= 20
if options.maximum_n_reads > READ_LINE_TO_INF:
options.maximum_n_reads = inf
else:
options.maximum_n_reads = int(options.maximum_n_reads)
if "--max-n-words" not in sys.argv:
if "embplant_mt" in options.organelle_type or "anonym" in options.organelle_type:
options.maximum_n_words *= 5
elif "embplant_nr" in options.organelle_type or "fungus_mt" in options.organelle_type or\
"fungus_nr" in options.organelle_type:
options.maximum_n_words /= 2
elif "animal_mt" in options.organelle_type:
options.maximum_n_words /= 2
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):
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 "--target-genome-size" not in sys.argv:
raw_default_value = int(str(options.target_genome_size))
options.target_genome_size = []
for go_t, sub_organelle_t in enumerate(options.organelle_type):
if sub_organelle_t == "embplant_mt":
options.target_genome_size.append(int(raw_default_value * 3))
elif sub_organelle_t == "fungus_mt":
options.target_genome_size.append(int(raw_default_value / 2))
elif sub_organelle_t in ("embplant_nr", "animal_mt", "fungus_nr"):
options.target_genome_size.append(int(raw_default_value / 10))
elif sub_organelle_t == "anonym":
ref_seqs = read_fasta(options.genes_fasta[go_t])[1]
options.target_genome_size.append(2 * sum([len(this_seq) for this_seq in ref_seqs]))
log_handler.info(
"Setting '--target-genome-size " + ",".join([str(t_s) for t_s in options.target_genome_size]) +
"' for estimating the word size value for anonym type.")
else:
options.target_genome_size.append(raw_default_value)
else:
temp_val_len = len(str(options.target_genome_size).split(","))
if temp_val_len != organelle_type_len:
log_handler.error("-F is followed with " + str(organelle_type_len) + " organelle types, " +
"while --target-genome-size is followed with " + str(temp_val_len) + " value(s)!\n")
exit()
try:
options.target_genome_size = [int(sub_size) for sub_size in str(options.target_genome_size).split(",")]
except ValueError:
log_handler.error("Invalid --target-genome-size value(s): " + str(options.target_genome_size))
exit()
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 in ("embplant_mt", "other_pt"):
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":
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 " + ",".join([str(t_s) for t_s in 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()
if "--max-extending-len" not in sys.argv:
options.max_extending_len = [] # -1 means auto
for go_t, seed_f in enumerate(options.seed_file):
# using auto as the default when using default seed files
# if os.path.realpath(seed_f) == os.path.join(_SEQ_DB_PATH, options.organelle_type[go_t] + ".fasta"):
# options.max_extending_len.append(-1)
# else:
# options.max_extending_len.append(inf)
options.max_extending_len.append(inf)
else:
temp_val_len = len(str(options.max_extending_len).split(","))
if temp_val_len != organelle_type_len:
log_handler.error("-F is followed with " + str(organelle_type_len) + " organelle types, " +
"while --max-extending-len is followed with " + str(temp_val_len) + " value(s)!\n")
exit()
try:
options.max_extending_len = [-1 if sub_size == "auto" else float(sub_size)
for sub_size in str(options.max_extending_len).split(",")]
except ValueError:
log_handler.error("Invalid --max-extending-len value(s): " + str(options.max_extending_len))
exit()
for sub_organelle_t in options.organelle_type:
if sub_organelle_t in ("fungus_mt", "animal_mt", "anonym"):
global MAX_RATIO_RL_WS
MAX_RATIO_RL_WS = 0.8
break
if not executable(os.path.join(options.which_bowtie2, "bowtie2")):
log_handler.error(os.path.join(options.which_bowtie2, "bowtie2") + " not accessible!")
exit()
if not executable(os.path.join(options.which_bowtie2, "bowtie2-build") + " --large-index"):
log_handler.error(os.path.join(options.which_bowtie2, "bowtie2-build") + " not accessible!")
exit()
# if not executable(os.path.join(options.which_bowtie2, "bowtie2-build-l")):
# log_handler.error(os.path.join(options.which_bowtie2, "bowtie2-build-l") + " not accessible!")
# exit()
run_slim = False
run_disentangle = False
if options.run_spades:
if options.which_spades:
if not executable(os.path.join(options.which_spades, "spades.py -h")):
raise Exception("spades.py not found/executable in " + options.which_spades + "!")
else:
run_slim = True
run_disentangle = True
else:
options.which_spades = ""
if not executable("spades.py -h"):
log_handler.error("spades.py not found in the PATH. "
"Adding SPAdes binary dir to the PATH or using \"--which-spades\" to fix this. "
"Now only get the reads and skip assembly.")
options.run_spades = False
else:
run_slim = True
run_disentangle = True
if not executable(os.path.join(options.which_blast, "blastn")):
log_handler.error(os.path.join(options.which_blast, "blastn") +
" not accessible! Slimming/Disentangling disabled!!\n")
run_slim = False
run_disentangle = False
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! Slimming/Disentangling disabled!!\n")
run_slim = False
run_disentangle = False
if lib_not_available:
log_handler.error("/".join(lib_not_available) + " not available! Disentangling disabled!!\n")
run_disentangle = False
options.rm_duplicates = int(options.rm_duplicates)
options.pre_grouped = int(options.pre_grouped)
if not options.rm_duplicates and options.pre_grouped:
log_handler.warning("removing duplicates was inactive, so that the pre-grouping was disabled.")
options.pre_grouped = False
if options.max_rounds and options.max_rounds < 1:
log_handler.warning("illegal maximum rounds! Set to infinite")
options.max_rounds = inf
if not options.max_rounds:
if not options.pre_grouped:
options.max_rounds = inf
else:
options.max_rounds = 1
for sub_organelle_t in options.organelle_type:
if sub_organelle_t in {"embplant_mt", "other_pt"}:
options.max_rounds = max(options.max_rounds, 30)
elif sub_organelle_t in {"embplant_nr", "animal_mt", "fungus_mt", "fungus_nr"}:
options.max_rounds = max(options.max_rounds, 10)
elif sub_organelle_t == "embplant_pt":
options.max_rounds = max(options.max_rounds, 15)
random.seed(options.random_seed)
try:
import numpy as np