def check_args(args):
'''
Check the input arguments.
'''
# initialize the control variable
OK = True
# check "input_vcf_file"
if args.input_vcf_file is None:
xlib.Message.print('error', '*** The VCF file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.input_vcf_file):
xlib.Message.print('error', f'*** The file {args.input_vcf_file} does not exist.')
OK = False
# check "imputed_md_id"
if args.imputed_md_id is None:
args.imputed_md_id = xlib.Const.DEFAULT_IMPUTED_MD_ID
# check "output_genotype_file"
if args.output_genotype_file is None:
xlib.Message.print('error', '*** The output genotype data file is not indicated in the input arguments.')
OK = False
# check "verbose"
if args.verbose is None:
args.verbose = xlib.Const.DEFAULT_VERBOSE
elif not xlib.check_code(args.verbose, xlib.get_verbose_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** verbose has to be {xlib.get_verbose_code_list_text()}.')
OK = False
if args.verbose.upper() == 'Y':
xlib.Message.set_verbose_status(True)
# check "trace"
if args.trace is None:
args.trace = xlib.Const.DEFAULT_TRACE
elif not xlib.check_code(args.trace, xlib.get_trace_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** trace has to be {xlib.get_trace_code_list_text()}.')
OK = False
if args.trace.upper() == 'Y':
xlib.Message.set_trace_status(True)
# check "tvi_list"
if args.tvi_list is None or args.tvi_list == 'NONE':
args.tvi_list = []
else:
args.tvi_list = xlib.split_literal_to_string_list(args.tvi_list)
# if there are errors, exit with exception
if not OK:
raise xlib.ProgramException('', 'P001')
def check_args(args):
'''
Check the input arguments.
'''
# initialize the control variable
OK = True
# check "ngshelper_database"
if args.ngshelper_database is None:
xlib.Message.print('error', '*** The NGShelper database is not indicated in the input arguments.')
OK = False
# check "vcf_file"
if args.vcf_file is None:
xlib.Message.print('error', '*** The VCF file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.vcf_file):
xlib.Message.print('error', f'*** The file {args.vcf_file} does not exist.')
OK = False
# check "sample_file"
if args.sample_file is None:
xlib.Message.print('error', '*** The sample file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.sample_file):
xlib.Message.print('error', f'*** The file {args.sample_file} does not exist.')
OK = False
# check "sp1_id"
if args.sp1_id is None:
xlib.Message.print('error', '*** The identification of the first species is not indicated in the input arguments.')
OK = False
# check "sp2_id"
if args.sp2_id is None:
xlib.Message.print('error', '*** The identification of the second species is not indicated in the input arguments.')
OK = False
# check "hybrid_id"
if args.hybrid_id is None:
args.hybrid_id = 'NONE'
# check "imputed_md_id"
if args.imputed_md_id is None:
args.imputed_md_id = xlib.Const.DEFAULT_IMPUTED_MD_ID
# check "new_md_id"
if args.new_md_id is None:
args.new_md_id = xlib.Const.DEFAULT_NEW_MD_ID
# check "allele_transformation"
if args.allele_transformation is None:
args.allele_transformation = 'NONE'
elif not xlib.check_code(args.allele_transformation, xlib.get_allele_transformation_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** The allele transformation has to be {xlib.get_allele_transformation_code_list_text()}.')
OK = False
else:
args.allele_transformation = args.allele_transformation.upper()
# check "verbose"
if args.verbose is None:
args.verbose = xlib.Const.DEFAULT_VERBOSE
elif not xlib.check_code(args.verbose, xlib.get_verbose_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** verbose has to be {xlib.get_verbose_code_list_text()}.')
OK = False
if args.verbose.upper() == 'Y':
xlib.Message.set_verbose_status(True)
# check "trace"
if args.trace is None:
args.trace = xlib.Const.DEFAULT_TRACE
elif not xlib.check_code(args.trace, xlib.get_trace_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** trace has to be {xlib.get_trace_code_list_text()}.')
OK = False
if args.trace.upper() == 'Y':
xlib.Message.set_trace_status(True)
# check "tvi_list"
if args.tvi_list is None or args.tvi_list == 'NONE':
args.tvi_list = []
else:
args.tvi_list = xlib.split_literal_to_string_list(args.tvi_list)
# check the identification set
if OK:
if args.sp1_id == args.sp2_id or \
args.hybrid_id is not None and (args.sp1_id == args.hybrid_id or args.sp2_id == args.hybrid_id):
xlib.Message.print('error', 'The identifications must be different.')
OK = False
# if there are errors, exit with exception
if not OK:
raise xlib.ProgramException('', 'P001')
def check_args(args):
'''
Check the input arguments.
'''
# initialize the control variable
OK = True
# check "vcf_file"
if args.vcf_file is None:
xlib.Message.print(
'error',
'*** The VCF file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.vcf_file):
xlib.Message.print('error',
f'*** The file {args.vcf_file} does not exist.')
OK = False
# check "sample_file"
if args.sample_file is None:
xlib.Message.print(
'error',
'*** The sample file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.sample_file):
xlib.Message.print('error',
f'*** The file {args.sample_file} does not exist.')
OK = False
# check "sp1_id"
if args.sp1_id is None:
xlib.Message.print(
'error',
'*** The identification of the first species is not indicated in the input arguments.'
)
OK = False
# check "sp2_id"
if args.sp2_id is None:
xlib.Message.print(
'error',
'*** The identification of the second species is not indicated in the input arguments.'
)
OK = False
# check "hybrid_id"
if args.hybrid_id is None:
args.hybrid_id = 'NONE'
# check "output_dir"
if args.output_dir is None:
xlib.Message.print(
'error',
'*** The output directy is not indicated in the input arguments.')
OK = False
elif not os.path.isdir(args.output_dir):
xlib.Message.print('error', '*** The output directy does not exist.')
OK = False
# check "variant_number_per_file"
if args.variant_number_per_file is None:
args.variant_number_per_file = xlib.Const.DEFAULT_VARIANT_NUMBER_PER_FILE
elif not xlib.check_int(args.variant_number_per_file, minimum=1):
xlib.Message.print(
'error',
'The variant number per file has to be an integer number greater than 0.'
)
OK = False
else:
args.variant_number_per_file = int(args.variant_number_per_file)
# check "allele_transformation"
if args.allele_transformation is None:
args.allele_transformation = 'NONE'
elif not xlib.check_code(args.allele_transformation,
xlib.get_allele_transformation_code_list(),
case_sensitive=False):
xlib.Message.print(
'error',
f'*** The allele transformation has to be {xlib.get_allele_transformation_code_list_text()}.'
)
OK = False
else:
args.allele_transformation = args.allele_transformation.upper()
# check "verbose"
if args.verbose is None:
args.verbose = xlib.Const.DEFAULT_VERBOSE
elif not xlib.check_code(
args.verbose, xlib.get_verbose_code_list(), case_sensitive=False):
xlib.Message.print(
'error',
f'*** verbose has to be {xlib.get_verbose_code_list_text()}.')
OK = False
if args.verbose.upper() == 'Y':
xlib.Message.set_verbose_status(True)
# check "trace"
if args.trace is None:
args.trace = xlib.Const.DEFAULT_TRACE
elif not xlib.check_code(
args.trace, xlib.get_trace_code_list(), case_sensitive=False):
xlib.Message.print(
'error', f'*** trace has to be {xlib.get_trace_code_list_text()}.')
OK = False
if args.trace.upper() == 'Y':
xlib.Message.set_trace_status(True)
# check "tvi_list"
if args.tvi_list is None or args.tvi_list == 'NONE':
args.tvi_list = []
else:
args.tvi_list = xlib.split_literal_to_string_list(args.tvi_list)
# check the identification set
if OK:
if args.sp1_id == args.sp2_id or \
args.hybrid_id is not None and (args.sp1_id == args.hybrid_id or args.sp2_id == args.hybrid_id):
xlib.Message.print('error',
'The identifications must be different.')
OK = False
# if there are errors, exit with exception
if not OK:
raise xlib.ProgramException('', 'P001')
def check_args(args):
'''
Check the input arguments.
'''
# initialize the control variable
OK = True
# check "input_vcf_file"
if args.input_vcf_file is None:
xlib.Message.print(
'error',
'*** The VCF file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.input_vcf_file):
xlib.Message.print(
'error', f'*** The file {args.input_vcf_file} does not exist.')
OK = False
# check "sample_file"
if args.sample_file is None:
xlib.Message.print(
'error',
'*** The sample file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.sample_file):
xlib.Message.print('error',
f'*** The file {args.sample_file} does not exist.')
OK = False
# check "fix"
if args.fix is None:
xlib.Message.print('error',
'*** Fix is not indicated in the input arguments.')
OK = False
elif not xlib.check_code(
args.fix, xlib.get_fix_code_list(), case_sensitive=False):
xlib.Message.print(
'error', f'*** fix has to be {xlib.get_fix_code_list_text()}.')
OK = False
else:
args.fix = args.fix.upper()
# check "scenario"
if args.scenario is None:
xlib.Message.print(
'error',
'*** The scenario is not indicated in the input arguments.')
OK = False
elif not xlib.check_code(args.scenario,
xlib.get_scenario_code_list(),
case_sensitive=False):
xlib.Message.print(
'error',
f'*** The scenario has to be {xlib.get_scenario_code_list_text()}.'
)
OK = False
# check "min_aa_percentage"
if args.min_aa_percentage is None:
xlib.Message.print(
'error',
'*** The minimum percent of alternative alleles per species is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_float(
args.min_aa_percentage, minimum=0.0, maximum=100.0):
xlib.Message.print(
'error',
'The minimum percent of alternative alleles per species has to be a float number between 0.0 and 100.0.'
)
OK = False
else:
args.min_aa_percentage = float(args.min_aa_percentage)
# check "min_md_imputation_percentage"
if args.min_md_imputation_percentage is None:
xlib.Message.print(
'error',
'*** The minimum percentage of missing data imputation to a new alternative allele per species is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_float(
args.min_md_imputation_percentage, minimum=0.0, maximum=100.0):
xlib.Message.print(
'error',
'The minimum percentage of missing data imputation to a new alternative allele per species has to be a float number between 0.0 and 100.0.'
)
OK = False
else:
args.min_md_imputation_percentage = float(
args.min_md_imputation_percentage)
# check "imputed_md_id"
if args.imputed_md_id is None:
args.imputed_md_id = xlib.Const.DEFAULT_IMPUTED_MD_ID
# check "sp1_id"
if args.sp1_id is None:
xlib.Message.print(
'error',
'*** The identification of the first species is not indicated in the input arguments.'
)
OK = False
# check "sp1_max_md_percentage"
if args.sp1_max_md_percentage is None:
xlib.Message.print(
'error',
'*** The maximum percentage of missing data of the first species is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_float(
args.sp1_max_md_percentage, minimum=0.0, maximum=100.0):
xlib.Message.print(
'error',
'The maximum percentage of missing data of the first species has to be a float number between 0.0 and 100.0.'
)
OK = False
else:
args.sp1_max_md_percentage = float(args.sp1_max_md_percentage)
# check "sp2_id"
if args.sp2_id is None:
xlib.Message.print(
'error',
'*** The identification of the second species is not indicated in the input arguments.'
)
OK = False
# check "sp2_max_md_percentage"
if args.sp2_max_md_percentage is None:
xlib.Message.print(
'error',
'*** The maximum percentage of missing data of the second species is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_float(
args.sp2_max_md_percentage, minimum=0.0, maximum=100.0):
xlib.Message.print(
'error',
'The maximum percentage of missing data of the second species has to be a float number between 0.0 and 100.0.'
)
OK = False
else:
args.sp2_max_md_percentage = float(args.sp2_max_md_percentage)
# check "hybrid_id"
if args.hybrid_id is None:
args.hybrid_id = 'NONE'
# check "min_afr_percentage"
if args.min_afr_percentage is None:
xlib.Message.print(
'error',
'*** The minimum percentage of allele frequency per species is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_float(
args.min_afr_percentage, minimum=0.0, maximum=100.0):
xlib.Message.print(
'error',
'The minimum percentage of allele frequency per species has to be a float number between 0.0 and 100.0.'
)
OK = False
else:
args.min_afr_percentage = float(args.min_afr_percentage)
# check "min_depth"
if args.min_depth is None:
args.min_depth = xlib.Const.DEFAULT_MIN_DEPTH
elif not xlib.check_int(args.min_depth, minimum=1):
xlib.Message.print(
'error',
'The minimum combined depth across samples has to be an integer number greater than or equal to 1.'
)
OK = False
else:
args.min_depth = int(args.min_depth)
# check "output_vcf_file"
if args.output_vcf_file is None:
xlib.Message.print(
'error',
'*** The output VCF file is not indicated in the input arguments.')
OK = False
# check "verbose"
if args.verbose is None:
args.verbose = xlib.Const.DEFAULT_VERBOSE
elif not xlib.check_code(
args.verbose, xlib.get_verbose_code_list(), case_sensitive=False):
xlib.Message.print(
'error',
f'*** verbose has to be {xlib.get_verbose_code_list_text()}.')
OK = False
if args.verbose.upper() == 'Y':
xlib.Message.set_verbose_status(True)
# check "trace"
if args.trace is None:
args.trace = xlib.Const.DEFAULT_TRACE
elif not xlib.check_code(
args.trace, xlib.get_trace_code_list(), case_sensitive=False):
xlib.Message.print(
'error', f'*** trace has to be {xlib.get_trace_code_list_text()}.')
OK = False
if args.trace.upper() == 'Y':
xlib.Message.set_trace_status(True)
# check "tvi_list"
if args.tvi_list is None or args.tvi_list == 'NONE':
args.tvi_list = []
else:
args.tvi_list = xlib.split_literal_to_string_list(args.tvi_list)
# check the identification set
if OK:
if args.sp1_id == args.sp2_id or \
args.hybrid_id is not None and (args.sp1_id == args.hybrid_id or args.sp2_id == args.hybrid_id):
xlib.Message.print('error',
'The identifications must be different.')
OK = False
# if there are errors, exit with exception
if not OK:
raise xlib.ProgramException('', 'P001')
def check_args(args):
'''
Check the input arguments.
'''
# initialize the control variable
OK = True
# initialize the list used to control variables with NONE values
none_variable_list = []
# check "toa_database"
if args.toa_database is None:
xlib.Message.print('error', '*** The TOA database is not indicated in the input arguments.')
OK = False
# check "transcriptome_file"
if args.transcriptome_file is None:
xlib.Message.print('error', '*** The transcriptome file is not indicated in the input arguments.')
OK = False
elif args.transcriptome_file.upper() == 'NONE':
args.transcriptome_file = args.transcriptome_file.upper()
none_variable_list.append('transcriptome_file')
elif not os.path.isfile(args.transcriptome_file):
xlib.Message.print('error', f'*** The file {args.transcriptome_file} does not exist.')
OK = False
# check "peptide_file"
if args.peptide_file is None:
xlib.Message.print('error', '*** The peptide file is not indicated in the input arguments.')
OK = False
elif args.peptide_file.upper() == 'NONE':
args.peptide_file = args.peptide_file.upper()
none_variable_list.append('peptide_file')
elif not os.path.isfile(args.peptide_file):
xlib.Message.print('error', f'*** The file {args.peptide_file} does not exist.')
OK = False
# check "dataset_list"
if args.dataset_list is None:
xlib.Message.print('error', '*** The list of annotation databases is not indicated in the input arguments.')
OK = False
elif args.dataset_list.upper() == 'NONE':
args.dataset_list = args.dataset_list.upper()
none_variable_list.append('dataset_list')
else:
args.dataset_list = xlib.split_literal_to_string_list(args.dataset_list)
# check "non_annotation_file_list"
if args.non_annotation_file_list is None:
xlib.Message.print('error', '*** The list of non annotated file paths is not indicated in the input arguments.')
OK = False
elif args.non_annotation_file_list.upper() == 'NONE':
args.non_annotation_file_list = args.non_annotation_file_list.upper()
none_variable_list.append('non_annotation_file_list')
else:
args.non_annotation_file_list = xlib.split_literal_to_string_list(args.non_annotation_file_list)
for non_annotation_file in args.non_annotation_file_list:
if not os.path.isfile(non_annotation_file):
xlib.Message.print('error', f'*** The file {non_annotation_file} does not exist.')
OK = False
# check relationships between "transcriptome_file", "peptide_file", "dataset_list" and "non_annotation_file_list"
if len(none_variable_list) not in [0, 4] and len(none_variable_list) == 1 and args.peptide_file != 'NONE':
xlib.Message.print('error', '*** all values of "transcriptome_file", "peptide_file", "dataset_list" and "non_annotation_file_list" have to be distinct to NONE or all values have to be NONE.')
OK = False
# check "annotation_file"
if args.annotation_file is None:
xlib.Message.print('error', '*** The annotation file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.annotation_file):
xlib.Message.print('error', f'*** The file {args.annotation_file} does not exist.')
OK = False
# check "type"
if args.type is None:
xlib.Message.print('error', '*** The type of annotation file is not indicated in the input arguments.')
OK = False
elif not xlib.check_code(args.type, xlib.get_type_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** The type of annotation file has to be {xlib.get_type_code_list_text()}.')
OK = False
else:
args.type = args.type.upper()
# check "stats_file"
if args.stats_file is None:
xlib.Message.print('error', '*** The statistics file is not indicated in the input arguments.')
OK = False
# check "verbose"
if args.verbose is None:
args.verbose = xlib.Const.DEFAULT_VERBOSE
elif not xlib.check_code(args.verbose, xlib.get_verbose_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** verbose has to be {xlib.get_verbose_code_list_text()}.')
OK = False
if args.verbose.upper() == 'Y':
xlib.Message.set_verbose_status(True)
# check "trace"
if args.trace is None:
args.trace = xlib.Const.DEFAULT_TRACE
elif not xlib.check_code(args.trace, xlib.get_trace_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** trace has to be {xlib.get_trace_code_list_text()}.')
OK = False
if args.trace.upper() == 'Y':
xlib.Message.set_trace_status(True)
# if there are errors, exit with exception
if not OK:
raise xlib.ProgramException('P001')
def check_args(args):
'''
Check the input arguments.
'''
# initialize the control variable
OK = True
# check "gff_file"
if args.gff_file is None:
xlib.Message.print(
'error',
'*** The input GFF file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.gff_file):
xlib.Message.print('error',
f'*** The file {args.gff_file} does not exist.')
OK = False
# check "gff_format"
if args.gff_format is None:
args.gff_format = 'GFF3'
elif args.gff_format.upper() != 'GFF3':
xlib.Message.print('error',
'*** The format of the GFF file has to be GFF3.')
OK = False
else:
args.gff_format = args.gff_format.upper()
# check "genome_file"
if args.genome_file is None:
xlib.Message.print(
'error',
'*** The FASTA genome file is not indicated in the input arguments.'
)
OK = False
elif not os.path.isfile(args.genome_file):
xlib.Message.print('error',
f'*** The file {args.genome_file} does not exist.')
OK = False
# check "rna_file"
if args.rna_file is None:
xlib.Message.print(
'error',
'*** The output FASTA file with the RNA sequences is not indicated in the input arguments.'
)
OK = False
# check "verbose"
if args.verbose is None:
args.verbose = xlib.Const.DEFAULT_VERBOSE
elif not xlib.check_code(
args.verbose, xlib.get_verbose_code_list(), case_sensitive=False):
xlib.Message.print(
'error',
f'*** verbose has to be {xlib.get_verbose_code_list_text()}.')
OK = False
if args.verbose.upper() == 'Y':
xlib.Message.set_verbose_status(True)
# check "trace"
if args.trace is None:
args.trace = xlib.Const.DEFAULT_TRACE
elif not xlib.check_code(
args.trace, xlib.get_trace_code_list(), case_sensitive=False):
xlib.Message.print(
'error', f'*** trace has to be {xlib.get_trace_code_list_text()}.')
OK = False
if args.trace.upper() == 'Y':
xlib.Message.set_trace_status(True)
# check "tvi_list"
if args.tvi_list is None or args.tvi_list == 'NONE':
args.tvi_list = []
else:
args.tvi_list = xlib.split_literal_to_string_list(args.tvi_list)
# if there are errors, exit with exception
if not OK:
raise xlib.ProgramException('', 'P001')
def check_args(args):
'''
Check the input arguments.
'''
# initialize the control variable
OK = True
# check "ngshelper_database"
if args.ngshelper_database is None:
xlib.Message.print(
'error',
'*** The NGShelper database is not indicated in the input arguments.'
)
OK = False
# check "sp1_id"
if args.sp1_id is None:
xlib.Message.print(
'error',
'*** The identification of the first species is not indicated in the input arguments.'
)
OK = False
# check "sp2_id"
if args.sp2_id is None:
xlib.Message.print(
'error',
'*** The identification of the second species is not indicated in the input arguments.'
)
OK = False
# check "hybrid_id"
if args.hybrid_id is None:
args.hybrid_id = 'NONE'
# check "max_separation"
if args.max_separation is None:
xlib.Message.print(
'error',
'*** The maximum separation between variants of the same intergenic fragment is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_int(args.max_separation, minimum=1):
xlib.Message.print(
'error',
'The maximum separation between variants of the same intergenic fragment has to be a integer number greater than 1.'
)
OK = False
else:
args.max_separation = int(args.max_separation)
# check "output_dir"
if args.output_dir is None:
xlib.Message.print(
'error',
'*** The output directy is not indicated in the input arguments.')
OK = False
elif not os.path.isdir(args.output_dir):
xlib.Message.print('error', '*** The output directy does not exist.')
OK = False
# check "verbose"
if args.verbose is None:
args.verbose = xlib.Const.DEFAULT_VERBOSE
elif not xlib.check_code(
args.verbose, xlib.get_verbose_code_list(), case_sensitive=False):
xlib.Message.print(
'error',
f'*** verbose has to be {xlib.get_verbose_code_list_text()}.')
OK = False
if args.verbose.upper() == 'Y':
xlib.Message.set_verbose_status(True)
# check "trace"
if args.trace is None:
args.trace = xlib.Const.DEFAULT_TRACE
elif not xlib.check_code(
args.trace, xlib.get_trace_code_list(), case_sensitive=False):
xlib.Message.print(
'error', f'*** trace has to be {xlib.get_trace_code_list_text()}.')
OK = False
if args.trace.upper() == 'Y':
xlib.Message.set_trace_status(True)
# check "tsi_list"
if args.tsi_list is None or args.tsi_list == 'NONE':
args.tsi_list = []
else:
args.tsi_list = xlib.split_literal_to_string_list(args.tsi_list)
# check the identification set
if OK:
if args.sp1_id == args.sp2_id or (args.sp1_id == args.hybrid_id
or args.sp2_id == args.hybrid_id):
xlib.Message.print('error',
'The identifications must be different.')
OK = False
# if there are errors, exit with exception
if not OK:
raise xlib.ProgramException('', 'P001')