def run_BacterialTyper(options):
## init time
start_time_total = time.time()
## debugging messages
global Debug
if (options.debug):
Debug = True
else:
Debug = False
##################################
### show help messages if desired
##################################
if (options.help_format):
## help_format option
help_info.help_fastq_format()
exit()
elif (options.help_BUSCO):
## information for BUSCO
BUSCO_caller.print_help_BUSCO()
exit()
elif (options.help_project):
## information for project
help_info.project_help()
exit()
elif (options.help_multiqc):
## information for Multiqc
multiQC_report.multiqc_help()
elif (options.help_Prokka):
## information for Prokka
annotation.print_list_prokka()
exit()
elif (options.help_Mash):
## information for Min Hash Software
min_hash_caller.helpMash()
exit()
elif (options.help_ARIBA):
## information for ARIBA
ariba_caller.help_ARIBA()
exit()
elif (options.help_trimm_adapters):
## help on trimm adapters
trimmomatic_call.print_help_adapters()
exit()
elif (options.help_KMA):
## information for KMA Software
species_identification_KMA.help_kma_database()
exit()
elif (options.help_MLSTar):
## information for KMA Software
MLSTar.help_MLSTar()
exit()
elif (options.help_PhiSpy):
## information for PhiSpy software
bacteriophage.help_PhiSpy()
exit()
elif (options.help_MGE_analysis):
## information for MGE module analysis
MGE.help_MGE_analysis()
exit()
elif (options.help_input_MGE):
## information for PhiSpy
MGE.help_input_MGE()
exit()
###
HCGB_aes.pipeline_header("BacterialTyper", ver=pipeline_version)
HCGB_aes.boxymcboxface("BacterialTyper analysis")
print("--------- Starting Process ---------")
HCGB_time.print_time()
## absolute path for in & out
input_dir = os.path.abspath(options.input)
outdir = ""
## set mode: project/detached
if (options.project):
outdir = input_dir
elif (options.detached):
outdir = os.path.abspath(options.output_folder)
def run_assembly(options):
"""Main function of the assemble module.
It assembles each sample using SPADES_ and checks quality using BUSCO_ software and database.
.. seealso:: This function depends on other BacterialTyper and HCGB functions called:
- :func:`BacterialTyper.scripts.BUSCO_caller.print_help_BUSCO`
- :func:`BacterialTyper.scripts.multiQC_report.multiqc_help`
- :func:`BacterialTyper.modules.qc.BUSCO_check`
- :func:`HCGB.sampleParser`
- :func:`HCGB.functions.aesthetics_functions`
- :func:`HCGB.functions.time_functions`
- :func:`HCGB.functions.main_functions`
- :func:`HCGB.functions.file_functions`
.. include:: ../../links.inc
"""
## init time
start_time_total = time.time()
## debugging messages
global Debug
if (options.debug):
Debug = True
else:
Debug = False
##################################
### show help messages if desired
##################################
if (options.help_format):
## help_format option
help_info.help_fastq_format()
exit()
elif (options.help_BUSCO):
## information for BUSCO
BUSCO_caller.print_help_BUSCO()
exit()
elif (options.help_project):
## information for project
help_info.project_help()
exit()
elif (options.help_multiqc):
## information for Multiqc
multiQC_report.multiqc_help()
exit()
### set as default paired_end mode
if (options.single_end):
options.pair = False
else:
options.pair = True
## message header
HCGB_aes.pipeline_header("BacterialTyper", ver=pipeline_version)
HCGB_aes.boxymcboxface("Assembly module")
print("--------- Starting Process ---------")
HCGB_time.print_time()
## absolute path for in & out
input_dir = os.path.abspath(options.input)
outdir = ""
## Project mode as default
project_mode = True
if (options.detached):
options.project = False
project_mode = False
outdir = os.path.abspath(options.output_folder)
else:
options.project = True
outdir = input_dir
## get files
pd_samples_retrieved = sampleParser.files.get_files(
options, input_dir, "trim", ['_trim'], options.debug)
## debug message
if (Debug):
print(colored("**DEBUG: pd_samples_retrieve **", 'yellow'))
print(pd_samples_retrieved)
## generate output folder, if necessary
print("\n+ Create output folder(s):")
if not options.project:
HCGB_files.create_folder(outdir)
outdir_dict = HCGB_files.outdir_project(outdir, options.project,
pd_samples_retrieved, "assemble",
options.debug)
### call assemble using spades
start_time_partial = start_time_total
start_time_partial_assembly = start_time_partial
## optimize threads
name_list = set(pd_samples_retrieved["name"].tolist())
threads_job = HCGB_main.optimize_threads(
options.threads, len(name_list)) ## threads optimization
max_workers_int = int(options.threads / threads_job)
## debug message
if (Debug):
HCGB_aes.debug_message("options.threads: " + str(options.threads),
"yellow")
HCGB_aes.debug_message("max_workers: " + str(max_workers_int),
"yellow")
HCGB_aes.debug_message("cpu_here: " + str(threads_job), "yellow")
# Group dataframe by sample name
sample_frame = pd_samples_retrieved.groupby(["name"])
# We can use a with statement to ensure threads are cleaned up promptly
print('+ Running modules SPADES...')
with concurrent.futures.ThreadPoolExecutor(
max_workers=max_workers_int) as executor:
## send for each sample
commandsSent = {
executor.submit(check_sample_assembly, name, outdir_dict[name],
sorted(cluster["sample"].tolist()), threads_job):
name
for name, cluster in sample_frame
}
for cmd2 in concurrent.futures.as_completed(commandsSent):
details = commandsSent[cmd2]
try:
data = cmd2.result()
except Exception as exc:
print('***ERROR:')
print(cmd2)
print('%r generated an exception: %s' % (details, exc))
## functions.timestamp
print("\n+ Assembly of all samples finished: ")
start_time_partial = HCGB_time.timestamp(start_time_partial_assembly)
##
if (assembly_stats):
###################
if Debug:
HCGB_aes.debug_message("assembly_stats dictionary", "yellow")
print(assembly_stats)
## create single file
get_assembly_stats_all(assembly_stats, outdir, Debug)
### symbolic links
print("+ Retrieve all genomes assembled...")
### BUSCO check assembly
if (options.no_BUSCO):
print()
else:
results = qc.BUSCO_check(outdir, outdir, options, start_time_partial,
"genome")
## print to file results
print("\n*************** Finish *******************")
start_time_partial = HCGB_time.timestamp(start_time_total)
print("+ Exiting Assembly module.")
return ()
def run_database(options):
## init time
start_time_total = time.time()
start_time_partial = start_time_total
## debugging messages
global Debug
if (options.debug):
Debug = True
print("[Debug mode: ON]")
else:
Debug = False
## message header
HCGB_aes.pipeline_header("BacterialTyper", ver=pipeline_version)
HCGB_aes.boxymcboxface("Database")
print("--------- Starting Process ---------")
HCGB_time.print_time()
kma_bin = set_config.get_exe("kma")
######################################################
## print further information if requested
if (options.help_ARIBA):
print("ARIBA databases information:")
ariba_caller.help_ARIBA()
exit()
elif (options.help_BUSCO):
BUSCO_caller.print_help_BUSCO()
exit()
elif (options.help_KMA):
species_identification_KMA.help_kma_database()
exit()
######################################################
## create folder
## absolute
options.path = os.path.abspath(options.path)
HCGB_files.create_folder(options.path)
#########
if Debug:
print(colored("DEBUG: absolute path folder: " + options.path,
'yellow'))
##########
## NCBI ##
##########
## if any NCBI options provided
if any([options.ID_file, options.descendant]):
## create folders
NCBI_folder = HCGB_files.create_subfolder('NCBI', options.path)
if (options.ID_file):
## get path and check if it is file
abs_path_file = os.path.abspath(options.ID_file)
if os.path.isfile(abs_path_file):
print()
HCGB_aes.print_sepLine("*", 50, False)
print("--------- Check NCBI ids provided ---------\n")
HCGB_aes.print_sepLine("*", 70, False)
## get file information
print("\t+ Obtaining information from file: %s" %
abs_path_file)
strains2get = HCGB_main.get_data(abs_path_file, ',', '')
dataBase_NCBI = database_generator.NCBI_DB(
strains2get, NCBI_folder, Debug)
#########
if Debug:
print(colored("DEBUG: NCBI data provided: ", 'yellow'))
print(options.ID_file)
## functions.timestamp
start_time_partial = HCGB_time.timestamp(start_time_partial)
## strains downloaded would be included to a kma index
## Get all entries belonging to this taxon provided
if (options.descendant):
#########
if Debug:
print(colored("DEBUG: NCBI descendant option: ON ", 'yellow'))
print()
HCGB_aes.print_sepLine("*", 70, False)
print(
"--------- Check descendant NCBI taxonomy ids provided ---------\n"
)
HCGB_aes.print_sepLine("*", 70, False)
## [TODO]
dataBase_NCBI = database_generator.NCBI_descendant(
options.descendant, NCBI_folder, Debug)
##############################################################
## update KMA database with NCBI information retrieved
##############################################################
print('\n\n+ Update database for later identification analysis...')
list_of_files = dataBase_NCBI['genome'].tolist()
kma_db = HCGB_files.create_subfolder('KMA_db', options.path)
genbank_kma_db = HCGB_files.create_subfolder('genbank', kma_db)
print('+ Database to update: ', genbank_kma_db)
species_identification_KMA.generate_db(list_of_files, 'genbank_KMA',
genbank_kma_db, 'new', 'batch',
Debug, kma_bin)
## time stamp
start_time_partial = HCGB_time.timestamp(start_time_total)
###############
## user_data ##
###############
if options.project_folder:
##
dataBase_user = pd.DataFrame()
## get absolute path
abs_project_folder = os.path.abspath(options.project_folder)
if os.path.exists(abs_project_folder):
#########
if Debug:
print(
colored("DEBUG: User provides folder containing project",
'yellow'))
print()
HCGB_aes.print_sepLine("*", 70, False)
print("--------- Check user provided project folder ---------")
HCGB_aes.print_sepLine("*", 70, False)
dataBase_user = database_user.update_database_user_data(
options.path, abs_project_folder, Debug, options)
else:
print(
colored(
"ERROR: Folder provided does not exists: %s" %
options.project_folder, 'red'))
exit()
##############################################################
## update KMA database with user_data information retrieved
##############################################################
print('\n\n+ Update database for later identification analysis...')
list_of_files = dataBase_user['genome'].tolist()
kma_db = HCGB_files.create_subfolder('KMA_db', options.path)
user_kma_db = HCGB_files.create_subfolder('user_data', kma_db)
print('+ Database to update: ', user_kma_db)
species_identification_KMA.generate_db(list_of_files, 'userData_KMA',
user_kma_db, 'new', 'batch',
Debug, kma_bin)
## time stamp
start_time_partial = HCGB_time.timestamp(start_time_total)
##########
## ARIBA
##########
print()
HCGB_aes.print_sepLine("*", 50, False)
print("--------- Check ARIBA parameters provided --------")
HCGB_aes.print_sepLine("*", 50, False)
if (options.no_ARIBA):
print("+ No ARIBA databases would be downloaded...")
#########
if Debug:
print(colored("DEBUG: No option ARIBA", 'yellow'))
else:
#functions.print_sepLine("*",50, False)
### ariba list databases
ariba_dbs_list = ['CARD', 'VFDB']
if (options.no_def_ARIBA):
ariba_dbs_list = options.ariba_dbs
else:
if (options.ariba_dbs):
ariba_dbs_list = ariba_dbs_list + options.ariba_dbs
ariba_dbs_list = set(ariba_dbs_list)
#########
if Debug:
print(colored("DEBUG: Option ARIBA", 'yellow'))
print(options.ariba_dbs)
ariba_caller.download_ariba_databases(ariba_dbs_list, options.path,
Debug, options.threads)
### ariba list databases
if (options.ariba_users_fasta):
print(
"+ Generate ARIBA database for databases provided: prepare fasta and metadata information"
)
#########
if Debug:
print(colored("DEBUG: Option user ARIBA db", 'yellow'))
print(ariba_users_fasta)
print(ariba_users_meta)
## [TODO]:
## ariba prepareref fasta and metadata
### timestamp
start_time_partial = HCGB_time.timestamp(start_time_partial)
#########
## kma ##
#########
print()
HCGB_aes.print_sepLine("*", 50, False)
print("--------- Check KMA parameters provided ----------")
kma_database = options.path + '/KMA_db'
HCGB_files.create_folder(kma_database)
## types: bacteria, archaea, protozoa, fungi, plasmids, typestrains
## downloads all "bacterial" genomes from KMA website
## kma: ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/
print(
"+ Retrieving information from: ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder website"
)
## KMA databases to use
## only user dbs
if (options.no_def_kma):
if (options.kma_dbs):
print("+ Only user databases selected will be indexed...")
else:
print("+ No databases selected.")
print(colored("ERROR: Please select a kma database.", 'red'))
exit()
## default dbs + user
else:
kma_dbs = ["bacteria", "plasmids"]
## default dbs + user
if (options.kma_dbs):
options.kma_dbs = options.kma_dbs + kma_dbs
options.kma_dbs = set(options.kma_dbs)
else:
options.kma_dbs = kma_dbs
#########
if Debug:
print(colored("DEBUG: options.kma_dbs", 'yellow'))
print(options.kma_dbs)
## Get databases
for db in options.kma_dbs:
print(colored("\n+ " + db, 'yellow'))
db_folder = HCGB_files.create_subfolder(db, kma_database)
species_identification_KMA.download_kma_database(db_folder, db, Debug)
### timestamp
start_time_partial = HCGB_time.timestamp(start_time_partial)
###########
## BUSCO ##
###########
if (options.BUSCO_dbs):
print()
HCGB_aes.print_sepLine("*", 50, False)
print("--------- Check BUSCO datasets provided ---------")
BUSCO_folder = HCGB_files.create_subfolder("BUSCO", options.path)
#########
if Debug:
print(colored("DEBUG: options.BUSCO_dbs", 'yellow'))
print(options.BUSCO_dbs)
print("+ BUSCO datasets would be downloaded when executed...")
#BUSCO_caller.BUSCO_retrieve_sets(options.BUSCO_dbs, BUSCO_folder)
### timestamp
start_time_partial = HCGB_time.timestamp(start_time_partial)
print("\n*************** Finish *******************\n")
start_time_partial = HCGB_time.timestamp(start_time_total)
print("+ Exiting Database module.\n")
return ()
def run_info(options):
## project help
if (options.help_project):
project_help()
exit()
## help_format option
if (options.help_format):
help_fastq_format()
exit()
## information for Prokka
if (options.help_Prokka):
annotation.print_list_prokka()
exit()
## information for BUSCO databases
if (options.help_BUSCO):
BUSCO_caller.print_help_BUSCO()
exit()
## information for ARIBA databases
if (options.help_ARIBA):
print("ARIBA databases information:")
ariba_caller.help_ARIBA()
exit()
## information for trimm adapters
if (options.help_trimm_adapters):
trimmomatic_call.print_help_adapters()
exit()
## information for Multiqc
if (options.help_multiqc):
multiQC_report.multiqc_help()
exit()
## information for KMA Software
if (options.help_KMA):
species_identification_KMA.help_kma_database()
exit()
## information for PhiSpy
if (options.help_PhiSpy):
bacteriophage.help_PhiSpy()
exit()
## information for MGE analysis
if (options.help_MGE_analysis):
MGE.help_MGE_analysis()
exit()
## information for MGE module
if (options.help_input_MGE):
MGE.help_input_MGE()
exit()
## information for MLSTar Software
if (options.help_MLSTar):
MLSTar.help_MLSTar()
exit()
## information for Min Hash Software
if (options.help_Mash):
min_hash_caller.helpMash()
exit()
## information for Snippy
if (options.help_Snippy):
variant_calling.help_Snippy()
exit()
## information for Dimob
if (options.help_Dimob):
genomic_island.help_Dimob()
exit()
def run_annotation(options):
## init time
start_time_total = time.time()
## debugging messages
global Debug
if (options.debug):
Debug = True
else:
Debug = False
##################################
### show help messages if desired
##################################
if (options.help_format):
## help_format option
sampleParser.help_format()
exit()
elif (options.help_BUSCO):
## information for BUSCO
BUSCO_caller.print_help_BUSCO()
exit()
elif (options.help_project):
## information for project
help_info.project_help()
exit()
elif (options.help_multiqc):
## information for Multiqc
multiQC_report.multiqc_help()
elif (options.help_Prokka):
## information for Prokka
annotation.print_list_prokka()
exit()
## set default
options.batch = False
###
HCGB_aes.pipeline_header("BacterialTyper", ver=pipeline_version)
HCGB_aes.boxymcboxface("Assembly annotation")
print("--------- Starting Process ---------")
HCGB_time.print_time()
## absolute path for in & out
input_dir = os.path.abspath(options.input)
outdir = ""
## Project mode as default
project_mode = True
if (options.detached):
options.project = False
project_mode = False
outdir = os.path.abspath(options.output_folder)
else:
options.project = True
outdir = input_dir
### symbolic links
print("+ Retrieve all genomes assembled...")
## get files
pd_samples_retrieved = sampleParser.files.get_files(
options, input_dir, "assembly", ["fna"], options.debug)
## debug message
if (Debug):
print(colored("**DEBUG: pd_samples_retrieve **", 'yellow'))
print(pd_samples_retrieved)
## generate output folder, if necessary
print("\n+ Create output folder(s):")
if not options.project:
HCGB_files.create_folder(outdir)
## for samples
outdir_dict = HCGB_files.outdir_project(outdir, options.project,
pd_samples_retrieved, "annot",
options.debug)
## annotate
print("+ Annotate assemblies using prokka:")
print("\t-Option: kingdom = ", options.kingdom, "; Annotation mode")
if options.genera == 'Other':
print(
"\t-Option: genera = Off; No genus-specific BLAST databases option provided"
)
else:
print("\t-Option: genera = ", options.genera,
"; Genus-specific BLAST databases option provided")
print("\t-Option: addgenes; Add 'gene' features for each 'CDS' feature")
print("\t-Option: addmrna; Add 'mRNA' features for each 'CDS' feature")
print("\t-Option: cdsrnaolap; Allow [tr]RNA to overlap CDS")
## optimize threads
name_list = set(pd_samples_retrieved["name"].tolist())
threads_job = HCGB_main.optimize_threads(
options.threads, len(name_list)) ## threads optimization
max_workers_int = int(options.threads / threads_job)
## debug message
if (Debug):
print(
colored("**DEBUG: options.threads " + str(options.threads) + " **",
'yellow'))
print(
colored("**DEBUG: max_workers " + str(max_workers_int) + " **",
'yellow'))
print(
colored("**DEBUG: cpu_here " + str(threads_job) + " **", 'yellow'))
## send for each sample
with concurrent.futures.ThreadPoolExecutor(
max_workers=max_workers_int) as executor:
commandsSent = {
executor.submit(annot_caller, row['sample'],
outdir_dict[row['name']], options, row['name'],
threads_job): index
for index, row in pd_samples_retrieved.iterrows()
}
for cmd2 in concurrent.futures.as_completed(commandsSent):
details = commandsSent[cmd2]
try:
data = cmd2.result()
except Exception as exc:
print('***ERROR:')
print(cmd2)
print('%r generated an exception: %s' % (details, exc))
## time stamp
start_time_partial = HCGB_time.timestamp(start_time_total)
## get folders
givenList = [v for v in outdir_dict.values()]
protein_files = []
print(
"+ Detail information for each sample could be identified in separate folders:"
)
for folder in givenList:
print('\t + ', folder)
protein_files.extend(
HCGB_main.retrieve_matching_files(folder, '.faa', Debug))
### report generation
if (options.skip_report):
print("+ No annotation report generation...")
else:
### report generation
HCGB_aes.boxymcboxface("Annotation report")
outdir_report = HCGB_files.create_subfolder("report", outdir)
PROKKA_report = HCGB_files.create_subfolder("annotation",
outdir_report)
print(
'\n+ A summary HTML report of each sample is generated in folder: %s'
% PROKKA_report)
## check if previously report generated
filename_stamp = PROKKA_report + '/.success'
done = 0
if os.path.isdir(PROKKA_report):
if os.path.isfile(filename_stamp):
stamp = HCGB_time.read_time_stamp(filename_stamp)
print(
colored(
"\tA previous report generated results on: %s" % stamp,
'yellow'))
done = 1
## generate report
if done == 0:
## get subdirs generated and call multiQC report module
multiQC_report.multiQC_module_call(givenList, "Prokka",
PROKKA_report, "-dd 2")
print(
'\n+ A summary HTML report of each sample is generated in folder: %s'
% PROKKA_report)
## success stamps
filename_stamp = PROKKA_report + '/.success'
stamp = HCGB_time.print_time_stamp(filename_stamp)
## time stamp
start_time_partial_BUSCO = HCGB_time.timestamp(start_time_total)
## Check each annotation using BUSCO
results = qc.BUSCO_check(input_dir, outdir, options,
start_time_partial_BUSCO, "proteins")
## print to file: results
print("\n*************** Finish *******************")
start_time_partial = HCGB_time.timestamp(start_time_total)
print("+ Exiting Annotation module.")
return ()
def run_QC(options):
## init time
start_time_total = time.time()
##################################
### show help messages if desired
##################################
if (options.help_format):
## help_format option
help_info.help_fastq_format()
exit()
elif (options.help_BUSCO):
## information for BUSCO
BUSCO_caller.print_help_BUSCO()
exit()
elif (options.help_project):
## information for project
help_info.project_help()
exit()
elif (options.help_multiqc):
## information for Multiqc
multiQC_report.multiqc_help()
exit()
## debugging messages
global Debug
if (options.debug):
Debug = True
else:
Debug = False
### set as default paired_end mode
if (options.single_end):
options.pair = False
else:
options.pair = True
## set main header
HCGB_aes.pipeline_header("BacterialTyper", ver=pipeline_version)
HCGB_aes.boxymcboxface("Quality check")
print("--------- Starting Process ---------")
HCGB_time.print_time()
## absolute path for in & out
input_dir = os.path.abspath(options.input)
outdir = ""
## Project mode as default
if (options.detached):
options.project = False
outdir = os.path.abspath(options.output_folder)
else:
options.project = True
outdir = input_dir
### option
if (options.raw_reads):
## get files
pd_samples_retrieved = sampleParser.files.get_files(
options, input_dir, "fastq", ("fastq", "fq", "fastq.gz", "fq.gz"),
options.debug)
fastqc(pd_samples_retrieved, outdir, options, start_time_total, "raw",
Debug)
elif (options.trim_reads):
## get files
pd_samples_retrieved = sampleParser.files.get_files(
options, input_dir, "trim", ['_trim'], options.debug)
fastqc(pd_samples_retrieved, outdir, options, start_time_total,
"trimmed", Debug)
elif (options.assembly):
BUSCO_check(input_dir, outdir, options, start_time_total, "genome")
elif (options.annotation):
BUSCO_check(input_dir, outdir, options, start_time_total, "proteins")
return ()
def BUSCO_check(input_dir, outdir, options, start_time_total, mode):
HCGB_aes.boxymcboxface("BUSCO Analysis Quality check")
## absolute path for in & out
database_folder = os.path.abspath(options.database)
## get files and get dir for each sample according to mode
if mode == 'genome':
pd_samples_retrieved = sampleParser.files.get_files(
options, input_dir, "assembly", ["fna"], options.debug)
if not options.project:
outdir = HCGB_files.create_subfolder("assembly_qc", outdir)
if options.debug:
print("** DEBUG: pd_samples_retrieved")
print(pd_samples_retrieved)
BUSCO_outdir_dict = HCGB_files.outdir_project(outdir, options.project,
pd_samples_retrieved,
"assemble_qc",
options.debug)
elif mode == 'proteins':
pd_samples_retrieved = sampleParser.files.get_files(
options, outdir, "annot", ["faa"], options.debug) ##
if not options.project:
outdir = HCGB_files.create_subfolder("annot_qc", outdir)
if options.debug:
print("** DEBUG: pd_samples_retrieved")
print(pd_samples_retrieved)
BUSCO_outdir_dict = HCGB_files.outdir_project(outdir, options.project,
pd_samples_retrieved,
"annot_qc",
options.debug)
## add column to dataframe
pd_samples_retrieved['busco_folder'] = ""
for index, row in pd_samples_retrieved.iterrows():
pd_samples_retrieved.at[index, 'busco_folder'] = BUSCO_outdir_dict[
row['name']]
## debug message
if (options.debug):
HCGB_aes.debug_message("df_samples_busco", 'yellow')
print(pd_samples_retrieved)
HCGB_aes.debug_message("BUSCO_outdir_dict", 'yellow')
print(BUSCO_outdir_dict)
## Check each using BUSCO
database_folder = os.path.abspath(options.database)
BUSCO_Database = HCGB_files.create_subfolder('BUSCO', database_folder)
if not os.path.exists(BUSCO_Database):
HCGB_files.create_folder(BUSCO_Database)
## call
(dataFrame_results, stats_results) = BUSCO_caller.BUSCO_call(
options.BUSCO_dbs, pd_samples_retrieved, BUSCO_Database,
options.threads, mode)
## debug message
if (options.debug):
HCGB_aes.debug_message("dataFrame_results", 'yellow')
HCGB_main.print_all_pandaDF(dataFrame_results)
## functions.timestamp
print("+ Quality control of all samples finished: ")
start_time_partial = HCGB_time.timestamp(start_time_total)
## multiqc report plot
if (options.skip_report):
print("+ No report generation...")
else:
print("\n+ Generating a report BUSCO plot.")
outdir_report = HCGB_files.create_subfolder("report", outdir)
## get subdirs generated and call multiQC report module
givenList = []
print(
"+ Detail information for each sample could be identified in separate folders."
)
## name folder according to mode
if mode == 'genome':
BUSCO_report = HCGB_files.create_subfolder("BUSCO_assembly",
outdir_report)
elif mode == 'proteins':
BUSCO_report = HCGB_files.create_subfolder("BUSCO_annot",
outdir_report)
## generate plots
print("+ Generate summarizing plots...")
BUSCO_caller.BUSCO_plots(dataFrame_results, BUSCO_report,
options.threads)
print('\n+ Check quality plots in folder: %s' % BUSCO_report)
## TODO
## Parse BUSCO statistics in dataframe (stats_results) for discarding samples if necessary
## given a cutoff, discard or advise to discard some samples
### print statistics
stats_results.to_csv(BUSCO_report + "/BUSCO_stats.csv")
name_excel = BUSCO_report + "/BUSCO_stats.xlsx"
writer = pd.ExcelWriter(name_excel, engine='xlsxwriter')
stats_results.to_excel(writer, sheet_name="BUSCO statistics")
writer.save()
print('\n+ Check quality statistics in folder: %s' % BUSCO_report)
return (dataFrame_results)