#!/opt/miniconda3/conda-bld/metawibele_1658851368973/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/python

"""
MeteWIBELE workflow: MeteWIBELE characterization workflow
1) clustering into protein families
2) protein family annotation
3) domain/motif annotation
4) abundance annotation
5) integration

Copyright (c) 2019 Harvard School of Public Health

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""

import sys
import os, fnmatch
import logging

# import the workflow class from anadama2
from anadama2 import Workflow

# import the library of MetaWIBELE tasks for characterization
try:
	from metawibele.tasks import characterization
except ImportError:
	sys.exit("CRITICAL ERROR: Unable to find the MetaWIBELE python package." +
		         " Please check your install.")

# import the utilities functions and config settings from MetaWIBELE
try:
	from metawibele import utilities, config
except ImportError:
	sys.exit("CRITICAL ERROR: Unable to find the MetaWIBELE python package." +
		         " Please check your install.")


VERSION = config.version

def parse_cli_arguments ():
	'''
	 Parses any command-line arguments passed into the workflow.
	the version number will appear when running this script with the "--version" option
	the description will appear when running this script with the "--help" option
	create a workflow instance, providing the version number and description
	'''
	
	tmp_output = os.path.abspath(config.working_dir)

	workflow = Workflow(version = VERSION, description = "A workflow for MetaWIBELE characterization", remove_options=["output"])

	# add the custom arguments to the workflow
	workflow.add_argument("threads",
	                      desc = "number of threads/cores for each task to use",
	                      default = None)
	workflow.add_argument("characterization-config",
	                      desc = "the configuration file of characterization analysis",
	                      default = None)
	workflow.add_argument("mspminer-config",
	                      desc = "the configuration file used by mspminer; [no] skip MSPminer-based taxonomic assignment",
	                      default = None)
	workflow.add_argument("bypass-clustering",
	                      desc = "do not cluster proteins into protein families",
	                      action = "store_true")
	workflow.add_argument("bypass-global-homology",
	                      desc = "do not annotate protein families based on global homology information",
	                      action = "store_true")
	workflow.add_argument("bypass-domain-motif",
	                      desc = "do not annotate protein families based on domain/motif information",
	                      action = "store_true")
	workflow.add_argument("bypass-interproscan",
	                      desc = "do not annotate protein families based on interproscan",
	                      action = "store_true")
	workflow.add_argument("bypass-pfam_to_go",
	                      desc = "do not annotate protein families based on pfam2go",
	                      action = "store_true")
	workflow.add_argument("bypass-domine",
	                      desc = "do not annotate protein families based on DOMINE database",
	                      action = "store_true")
	workflow.add_argument("bypass-sifts",
	                      desc = "do not annotate protein families based on SIFTS database",
	                      action = "store_true")
	workflow.add_argument("bypass-expatlas",
	                      desc = "do not annotate protein families based on Expression Atlas database",
	                      action = "store_true")
	workflow.add_argument("bypass-psortb",
	                      desc = "do not annotate protein families based on psortb",
	                      action = "store_true")
	workflow.add_argument("bypass-abundance",
	                      desc = "do not annotate protein families based on abundance information",
	                      action = "store_true")
	workflow.add_argument("bypass-mspminer",
	                      desc = "do not annotate protein families based on MSPminer",
	                      action = "store_true")
	workflow.add_argument("bypass-maaslin",
	                      desc = "do not annotate protein families based on MaAsLin2",
	                      action = "store_true")
	workflow.add_argument("split-number",
	                      desc="indicates number of spliting files for annotation based on sequence information",
	                      default = None)
	workflow.add_argument("bypass-integration",
	                      desc = "do not integrate annotations for protein families",
	                      action = "store_true")
	workflow.add_argument("study",
	                      desc="specify the study name", 
	                      default = None)
	workflow.add_argument("basename",
	                      desc="specify the basename for output files", 
	                      default = None)
	workflow.add_argument("input-sequence",
	                      desc="input the sequence file for gene families (non-redundant catalogs)",
	                      required = True)
	workflow.add_argument("input-count",
	                      desc="input the count file for gene families (non-redundant catalogs)",
	                      required = True)
	workflow.add_argument("input-metadata",
	                      desc="input the metadata file", 
	                      required = True)
	workflow.add_argument("output",
	                      desc = "provide an output folder which the workflow database and log is written. By default, thet be written to the anadama2 folder of users' working directory",
	                      default = tmp_output)

	return workflow



def get_method_config (config_file):
	'''
	:param config_file:
	:return: config info for each analysis
	'''
	config.logger.info ("###### Start get_method_config module ######")

	config_items = config.read_user_edit_config_file(config_file)
	family_conf = {}
	domain_motif_conf = {}
	abundance_conf = {}
	integration_conf = {}
	values = ["yes", "no", "Yes", "No"]

	if "global_homology" in config_items:
		for name in config_items["global_homology"].keys():
			myvalue = config_items["global_homology"][name]
			if not myvalue in values:
				config.logger.info ('ERROR! The config value can not be recognized. Please check your config file!')
				continue
			family_conf[name] = myvalue
		# for each method

	if "domain_motif" in config_items:
		for name in config_items["domain_motif"].keys():
			myvalue = config_items["domain_motif"][name]
			if not myvalue in values:
				config.logger.info ('ERROR! The config value can not be recognized. Please check your config file!')
				continue
			domain_motif_conf[name] = myvalue
		# for each method

	if "abundance" in config_items:
		for name in config_items["abundance"].keys():
			myvalue = config_items["abundance"][name]
			abundance_conf[name] = myvalue
		# for each method

	if "integration" in config_items:
		for name in config_items["integration"].keys():
			myvalue = config_items["integration"][name]
			if not myvalue in values:
				config.logger.info ('ERROR! The config value can not be recognized. Please check your config file!')
				continue
			integration_conf[name] = myvalue
		# for each method

	config.logger.info("###### Finish get_method_config module ######")

	return family_conf, domain_motif_conf, abundance_conf, integration_conf



def main(workflow):
	'''
	Characterization of protein families
	'''

	# get arguments
	args = workflow.parse_args()
	tmps_dir = os.path.join (os.getcwd(), "temp")
	tmps_dir = os.path.abspath(tmps_dir)
	#if os.path.isdir(tmps_dir):
	#	os.system("rm -rf " + tmps_dir)

	# get configuration info
	default_characterization_conf = os.path.join(config.config_directory, "characterization.cfg")
	if args.characterization_config:
		args.characterization_config = os.path.abspath(args.characterization_config)
	else:
		args.characterization_config = default_characterization_conf
	config.logger.info ("The config file used for characterization: " + args.characterization_config)
	
	# update configurations of characterization
	family_conf, domain_motif_conf, abundance_conf, integration_conf = get_method_config(args.characterization_config)
	if args.threads:
		args.threads = int(args.threads)
	else:
		args.threads = int(config.threads)
	if args.split_number:
		args.split_number = int(args.split_number)
	else:
		args.split_number = int(config.split_number)
	if args.mspminer_config:
		if args.mspminer_config != "no" and args.mspminer_config != "No":
			abundance_conf["mspminer"] = os.path.abspath(args.mspminer_config)
		else:
			abundance_conf["mspminer"] = args.mspminer_config
	else:
		abundance_conf["mspminer"] = config.mspminer
	if args.bypass_mspminer:
		abundance_conf["mspminer"] = "no"

	if args.bypass_global_homology:
		family_conf["uniref"] = "no"
	if args.bypass_interproscan:
		domain_motif_conf["interproscan"] = "no"
		domain_motif_conf["pfam2go"] = "no"
		domain_motif_conf["domine"] = "no"
		domain_motif_conf["sifts"] = "no"
		domain_motif_conf["expatlas"] = "no"
	if args.bypass_pfamtogo:
		domain_motif_conf["pfam2go"] = "no"
	if args.bypass_domine:
		domain_motif_conf["domine"] = "no"
	if args.bypass_sifts:
		domain_motif_conf["sifts"] = "no"
	if args.bypass_expatlas:
		domain_motif_conf["expatlas"] = "no"
	if args.bypass_psortb:
		domain_motif_conf["psortb"] = "no"
	if "".join(config.phenotype) == "none":
		abundance_conf["dna_da"] = "no"
	if args.bypass_maaslin:
		abundance_conf["dna_da"] = "no"

	# get all input files
	gene_catalog_seq = config.gene_catalog_prot
	gene_catalog_count = config.gene_catalog_count
	metadata = config.metadata
	study = config.study
	basename = config.basename
	if args.input_sequence:
		gene_catalog_seq = os.path.abspath(args.input_sequence)
	if args.input_count:
		gene_catalog_count = os.path.abspath(args.input_count)
	if args.input_metadata:
		metadata = os.path.abspath(args.input_metadata)
	if args.study:
		study = args.study
	if args.basename:
		basename = args.basename
	if not os.path.isfile(gene_catalog_seq):
		sys.exit("Please input your sequence file for gene families!")
	if not os.path.isfile(gene_catalog_count):
		sys.exit("Please input your count file for gene families!")
	if not os.path.isfile(metadata):
		sys.exit("Please input your metadata file!")

	# get all output files
	output_dir = config.annotation_dir
	output_dir = os.path.abspath(output_dir)
	if args.output:
		output_dir = os.path.abspath(args.output)
	annotation_dir = os.path.join(output_dir, "finalized")
	os.system("mkdir -p " + annotation_dir)
	protein_family = os.path.join(annotation_dir, basename + "_proteinfamilies.clstr")
	protein_family_seq = os.path.join(annotation_dir, basename + "_proteinfamilies.centroid.faa")
	protein_family_relab = os.path.join(annotation_dir, basename + "_proteinfamilies_nrm.tsv")
	protein_family_ann = os.path.join(annotation_dir, basename + "_proteinfamilies_annotation.tsv")
	protein_family_attr = os.path.join(annotation_dir, basename + "_proteinfamilies_annotation.attribute.tsv")
	uniref_taxonomy_family = os.path.join(annotation_dir, basename + "_proteinfamilies_annotation.uniref90_annotation.tsv")
	uniref_taxonomy = os.path.join(annotation_dir, basename + "_protein_annotation.uniref90_annotation.tsv")
	taxonomy_annotation_family = os.path.join(annotation_dir, basename + "_proteinfamilies_annotation.taxonomy.tsv")
	taxonomy_annotation = os.path.join(annotation_dir, basename + "_protein_annotation.taxonomy.tsv")
	protein_family_ann_list = {}
	protein_ann_list = {}


	#### STEP #1: clustering ####
	# if clustering action is provided, then cluster proteins into protein families
	if not args.bypass_clustering:
		config.logger.info ("Start to run clustering module......")
		myprotein_family, myprotein_family_output_folder = characterization.clustering (workflow, gene_catalog_seq,
		                                                                                args.threads,
		                                                                                output_dir, protein_family, protein_family_seq)

	else:
		config.logger.info ("WARNING! Bypass module: the clustering module is skipped......")

	#### STEP #2: global-homology annotation ####
	# if global-homology action is provided, then directly extract annotations from database (UniProt)
	if not args.bypass_global_homology:
		config.logger.info ("Start to run global-homology annotation module......")
		if family_conf["uniref"] == "no":
			config.logger.info ("WARNING! Bypass module: the global-homology annotation module is skipped......")
		myprotein_family_ann, myprotein_ann, homology_output_folder = characterization.global_homology_annotation (workflow, family_conf,
		                                                                                                          gene_catalog_seq, metadata, study, basename, args.threads,
																												  output_dir, uniref_taxonomy_family, uniref_taxonomy,
		                                                                                                          protein_family_ann_list, protein_ann_list, protein_family, protein_family_seq)
	else:
		config.logger.info ("WARNING! Bypass module: the global-homology annotation module is skipped......")

	#### STEP #3: domain-motif annotation ####
	# if domain-motif action is provided, then do annotations based on sequence information
	if not args.bypass_domain_motif:
		config.logger.info ("Start to run domain-motif annotation module......")
		if domain_motif_conf["interproscan"] == "no":
			config.logger.info ("WARNING! Bypass module: the interproscan annotation module is skipped......")
		if domain_motif_conf["pfam2go"] == "no":
			config.logger.info ("WARNING! Bypass module: the pfam2go annotation module is skipped......")
		if domain_motif_conf["domine"] == "no":
			config.logger.info ("WARNING! Bypass module: the DDI annotation module is skipped......")
		if domain_motif_conf["sifts"] == "no":
			config.logger.info ("WARNING! Bypass module: the DDI-SIFTS annotation module is skipped......")
		if domain_motif_conf["expatlas"] == "no":
			config.logger.info ("WARNING! Bypass module: the DDI-ExpAtlas annotation module is skipped......")
		if domain_motif_conf["psortb"] == "no":
			config.logger.info ("WARNING! Bypass module: the psortb annotation module is skipped......")
		myprotein_family_ann, myprotein_ann, sequence_output_folder = characterization.domain_motif_annotation (workflow, domain_motif_conf,
		                                                                                                          gene_catalog_seq,
		                                                                                                          args.split_number, metadata, study, basename, args.threads,
		                                                                                                          output_dir, protein_family_ann_list, protein_ann_list, protein_family, protein_family_seq)

	else:
		config.logger.info ("WARNING! Bypass module: the domain-motif annotation module is skipped......")

	#### STEP #4: abundance annotation ####
	# if abundance action is provided, then do annotations based on abundance information
	if not args.bypass_abundance:
		config.logger.info ("Start to run abundance annotation module......")
		if abundance_conf["mspminer"] == "no":
			config.logger.info ("WARNING! Bypass module: the MSPminer annotation module is skipped......")
		if abundance_conf["dna_da"] == "no":
			config.logger.info ("WARNING! Bypass module: the MaAsLin2 annotation module is skipped......")
		myprotein_family_ann, myprotein_ann, abundance_output_folder = characterization.abundance_annotation (workflow, abundance_conf,
		                                                                                                             gene_catalog_seq, gene_catalog_count,
		                                                                                                            uniref_taxonomy_family, uniref_taxonomy,
		                                                                                                            args.split_number, metadata, study, basename, args.threads,
		                                                                                                            output_dir, protein_family, protein_family_relab, taxonomy_annotation_family, taxonomy_annotation,
		                                                                                                            protein_family_ann_list, protein_ann_list)
	else:
		config.logger.info ("WARNING! Bypass module: the abundance annotation module is skipped......")
	
	#### STEP #4: integrate annotations ####
	if not args.bypass_integration:
		config.logger.info ("Start to run integration annotation module......")
		myprotein_family_ann, myprotein_family_attr, annotation_output_folder = characterization.integration_annotation (workflow, integration_conf,
		                                                                                                               protein_family_ann_list, protein_ann_list,
		                                                                                                               uniref_taxonomy_family, uniref_taxonomy,
		                                                                                                               taxonomy_annotation_family, taxonomy_annotation,
		                                                                                                               metadata, study, basename, protein_family, args.threads,
		                                                                                                               annotation_dir, protein_family_ann, protein_family_attr)
	else:
		config.logger.info ("WARNING! Bypass module: the integration annotation module is skipped......")

	## start the workflow
	workflow.go()



if __name__ == "__main__":
	main(parse_cli_arguments())



