def check_args(args):
'''
Check the input arguments.
'''
# initialize the control variable
OK = True
# 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_type2_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** The type of annotation file has to be {xlib.get_type2_code_list_text()}.')
OK = False
else:
args.type = args.type.upper()
# check "score_file"
if args.score_file is None:
xlib.Message.print('error', '*** The sequence score file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.score_file):
xlib.Message.print('error', f'*** The file {args.score_file} does not exist.')
OK = False
# check "go_file"
if args.go_file is None:
xlib.Message.print('error', '*** The file with GO terms per sequence 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 "input_gff_file"
if args.input_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.input_gff_file):
xlib.Message.print('error', f'*** The file {args.input_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 "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 "output_gff_file"
if args.output_gff_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)
# 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 "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 "table_group"
if args.table_group is None:
xlib.Message.print(
'error',
'*** The table group is not indicated in the input arguments.')
OK = False
elif not xlib.check_code(args.table_group,
xlib.get_table_group_code_list(),
case_sensitive=False):
xlib.Message.print(
'error',
f'*** The table group has to be {xlib.get_table_group_code_list_text()}.'
)
OK = False
else:
args.table_group = args.table_group.lower()
# 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 "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 "alignment_file"
if args.alignment_file is None:
xlib.Message.print('error', '*** The alignment file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.alignment_file):
xlib.Message.print('error', f'*** The file {args.alignment_file} 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)
# if there are errors, exit with exception
if not OK:
raise xlib.ProgramException('', 'P001')
def check_args(args):
'''
Verity the input arguments data.
'''
# initialize the control variable
OK = True
# check "fasta_file"
if args.fasta_file is None:
xlib.Message.print(
'error',
'*** The input FASTA file is not indicated in the input arguments.'
)
OK = False
elif not os.path.isfile(args.fasta_file):
xlib.Message.print('error',
f'*** The file {args.fasta_file} does not exist.')
OK = False
# check the output_file value
if args.output_file is None:
xlib.Message.print(
'error',
'*** A output file where filtered transcripts will be saved is not indicated in the input arguments.'
)
OK = False
else:
try:
if not os.path.exists(os.path.dirname(args.output_file)):
os.makedirs(os.path.dirname(args.output_file))
except Exception as e:
xlib.Message.print('error', f'*** EXCEPTION: "{e}".')
xlib.Message.print(
'error',
f'*** The directory {os.path.dirname(args.output_file)} of the file {args.output_file} is not valid.'
)
OK = False
# check the minlen value
if args.minlen is None:
args.minlen = xlib.Const.DEFAULT_MINLEN
elif not xlib.check_int(args.minlen, minimum=1):
xlib.Message.print(
'error',
'*** The minlen has to be a integer number greater than 0.')
OK = False
else:
args.minlen = int(args.minlen)
# check the maxlen value
if args.maxlen is None:
args.maxlen = xlib.Const.DEFAULT_MAXLEN
elif not xlib.check_int(args.maxlen, minimum=1):
xlib.Message.print(
'error',
'*** The maxlen has to be a integer number greater than 0.')
OK = False
else:
args.maxlen = int(args.maxlen)
# 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 if maxlen value is greater or equal than minlen value
if OK:
if args.maxlen < args.minlen:
xlib.Message.print(
'error',
'*** The maxlen value has to be greater than or equal to minlen.'
)
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 "purge_operation"
is_ok_purge_operation = False
if args.purge_operation is None:
xlib.Message.print(
'error',
'*** The purge operation is not indicated in the input arguments.')
OK = False
elif not xlib.check_code(args.purge_operation,
xlib.get_vcf_purge_code_list(),
case_sensitive=False):
xlib.Message.print(
'error',
f'*** The purge operation has to be {xlib.get_vcf_purge_code_list_text()}.'
)
OK = False
else:
args.purge_operation = args.purge_operation.upper()
is_ok_purge_operation = True
# check "value"
if args.value is None:
xlib.Message.print(
'error',
'*** The value to perform the purge operation is not indicated the input arguments.'
)
OK = False
# check "new_value"
if args.new_value is None and is_ok_purge_operation and args.purge_operation == 'CHAVAR':
xlib.Message.print(
'error',
'*** The new value to perform the purge operation is not indicated the input arguments.'
)
OK = False
elif args.new_value is None:
args.new_value = ' NONE'
# check "output_purged_file"
if args.output_purged_file is None:
xlib.Message.print(
'error',
'*** The purged 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):
'''
Verity the input arguments data.
'''
# initialize the control variable
OK = True
# check "cos_file"
if args.cos_file is None:
xlib.Message.print(
'error',
'*** The input COS file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.cos_file):
xlib.Message.print('error',
f'*** The file {args.cos_file} does not exist.')
OK = False
# check "ssr_file"
if args.ssr_file is None:
xlib.Message.print(
'error',
'*** The input SSR file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.ssr_file):
xlib.Message.print('error',
f'*** The file {args.ssr_file} does not exist.')
OK = False
# check the output_file value
if args.output_file is None:
xlib.Message.print(
'error',
'*** A output file where filtered SSR will be saved is not indicated in the input arguments.'
)
OK = False
else:
try:
if not os.path.exists(os.path.dirname(args.output_file)):
os.makedirs(os.path.dirname(args.output_file))
except Exception as e:
xlib.Message.print('error', f'*** EXCEPTION: "{e}".')
xlib.Message.print(
'error',
f'*** The directory {os.path.dirname(args.output_file)} of the file {args.output_file} is not valid.'
)
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 "app"
if args.app is None:
xlib.Message.print(
'error',
'*** The application is not indicated in the input arguments.')
OK = False
elif not xlib.check_code(
args.app, xlib.get_go_app_code_list(), case_sensitive=False):
xlib.Message.print(
'error',
f'*** The application has to be {xlib.get_go_app_code_list_text()}.'
)
OK = False
else:
args.app = args.app.upper()
# 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 "ontology_file"
if args.ontology_file is None:
xlib.Message.print(
'error',
'*** The ontology file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.ontology_file):
xlib.Message.print(
'error', f'*** The file {args.ontology_file} does not exist.')
OK = False
# 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)
# 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 "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 "header"
if args.header is None:
args.header = xlib.Const.DEFAULT_HEADER
elif not xlib.check_code(
args.header, xlib.get_header_code_list(), case_sensitive=False):
xlib.Message.print(
'error',
f'*** header has to be {xlib.get_header_code_list_text()}.')
OK = False
else:
args.header = args.header.upper()
# check "record_number_per_file"
if args.record_number_per_file is None:
args.record_number_per_file = xlib.Const.DEFAULT_RNUM
elif not xlib.check_int(args.record_number_per_file, minimum=1):
xlib.Message.print(
'error',
'*** The record number per splitted file has to be an integer number greater than 0.'
)
OK = False
else:
args.record_number_per_file = int(args.record_number_per_file)
# 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):
'''
Verity the input arguments data.
'''
# initialize the control variable
OK = True
# check the assembly_software_code value
if args.assembly_software_code is None:
xlib.Message.print(
'error',
'*** The assembly software that generated the transcritpme file is not indicated in the input arguments.'
)
OK = False
elif args.assembly_software_code not in [
xlib.Const.AS_TRINITY_CODE, xlib.Const.AS_SOAPDENOVOTRANS_CODE,
xlib.Const.AS_GENERATED_BY_NGSCLOUD
]:
xlib.Message.print(
'error',
f'*** {args.assembly_software_code} is not a valid code of assembly software.'
)
OK = False
# check the transcriptome_file value
if args.transcriptome_file is None:
xlib.Message.print(
'error',
'*** A transcritpme file in Fasta format is not indicated in the input arguments.'
)
OK = False
elif not os.path.isfile(args.transcriptome_file):
xlib.Message.print(
'error', f'*** The file {args.transcriptome_file} does not exist.')
OK = False
# check the score_file value
if args.score_file is None:
xlib.Message.print(
'error',
'*** A score file where RSEM-EVAL (DETONATE package) saved the score of the transcriptome file is not indicated in the input arguments.'
)
OK = False
elif not os.path.isfile(args.score_file):
xlib.Message.print('error',
f'*** The file {args.score_file} does not exist.')
OK = False
# check the output_file value
if args.output_file is None:
xlib.Message.print(
'error',
'*** A output file where filtered transcripts will be saved is not indicated in the input arguments.'
)
OK = False
else:
try:
if not os.path.exists(os.path.dirname(args.output_file)):
os.makedirs(os.path.dirname(args.output_file))
except Exception as e:
xlib.Message.print(
'error',
f'*** The directory {os.path.dirname(args.output_file)} of the file {args.output_file} is not valid.'
)
OK = False
# check the minlen value
if args.minlen is None:
args.minlen = xlib.Const.DEFAULT_MINLEN
elif not xlib.check_int(args.minlen, minimum=1):
xlib.Message.print(
'error',
'*** The minlen has to be a integer number greater than 0.')
OK = False
else:
args.minlen = int(args.minlen)
# check the maxlen value
if args.maxlen is None:
args.maxlen = xlib.Const.DEFAULT_MAXLEN
elif not xlib.check_int(args.maxlen, minimum=1):
xlib.Message.print(
'error',
'*** The maxlen has to be a integer number greater than 0.')
OK = False
else:
args.maxlen = int(args.maxlen)
# check the minFPKM value
if args.minFPKM is None:
args.minFPKM = xlib.Const.DEFAULT_MINFPKM
elif not xlib.check_float(args.minFPKM, minimum=0.0):
print(
'*** FPKM has to be a float number greater than or equal to 0.0.')
OK = False
else:
args.minFPKM = float(args.minFPKM)
# check the minTPM value
if args.minTPM is None:
args.minTPM = xlib.Const.DEFAULT_MINTPM
elif not xlib.check_float(args.minTPM, minimum=0.0):
print(
'*** FPKM has to be a float number greater than or equal to 0.0.')
OK = False
else:
args.minTPM = float(args.minTPM)
# 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 if maxlen value is greater or equal than minlen value
if OK:
if args.maxlen < args.minlen:
xlib.Message.print(
'error',
'*** The maxlen value has to be greater than or equal to minlen.'
)
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 input 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 "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 "flanking_region_file"
if args.flanking_region_file is None:
xlib.Message.print(
'error',
'*** The FASTA file with flanking regions is not indicated in the input arguments.'
)
OK = False
# check "nucleotide_number"
if args.nucleotide_number is None:
args.nucleotide_number = xlib.Const.DEFAULT_NUCLEOTIDE_NUMBER
elif not xlib.check_int(args.nucleotide_number, 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.nucleotide_number = int(args.nucleotide_number)
# 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 "simhyb_file"
if args.simhyb_file is None:
xlib.Message.print(
'error',
'*** The SimHyb file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.simhyb_file):
xlib.Message.print('error',
f'*** The file {args.simhyb_file} does not exist.')
OK = False
# check "header_row_number"
if args.header_row_number is None:
xlib.Message.print(
'error',
'*** The header row number in the SimHyb file is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_int(args.header_row_number, minimum=0):
xlib.Message.print(
'error',
'The header row number in the SimHyb file has to be an integer number greater than or equalt to 0.'
)
OK = False
else:
args.header_row_number = int(args.header_row_number)
# check "structure_file"
if args.structure_file is None:
xlib.Message.print(
'error',
'*** The converted Structure 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 "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 "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')
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
# check "fasta_file_1"
if args.fasta_file_1 is None:
xlib.Message.print(
'error',
'*** The first FASTA file is not indicated in the input arguments.'
)
OK = False
elif not os.path.isfile(args.fasta_file_1):
xlib.Message.print(
'error', f'*** The file {args.fasta_file_1} does not exist.')
OK = False
# check "fasta_file_2"
if args.fasta_file_2 is None:
xlib.Message.print(
'error',
'*** The second FASTA file is not indicated in the input arguments.'
)
OK = False
elif not os.path.isfile(args.fasta_file_2):
xlib.Message.print(
'error', f'*** The file {args.fasta_file_2} does not exist.')
OK = False
# check "merged_file"
if args.merged_file is None:
xlib.Message.print(
'error',
'*** The merged file is not indicated in the input arguments.')
OK = False
# check "merger_operation"
if args.merger_operation is None:
xlib.Message.print(
'error',
'*** The merger operation is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_code(args.merger_operation,
xlib.get_fasta_merger_operation_code_list(),
case_sensitive=False):
xlib.Message.print(
'error',
f'*** The merger operation has to be {xlib.get_fasta_merger_operation_code_list_text()}.'
)
OK = False
else:
args.merger_operation = args.merger_operation.upper()
# check "toa_transcriptome_relationship_file"
if args.toa_transcriptome_relationship_file is None:
args.toa_transcriptome_relationship_file = 'NONE'
elif args.toa_transcriptome_relationship_file.upper() == 'NONE':
args.toa_transcriptome_relationship_file = args.toa_transcriptome_relationship_file.upper(
)
elif not os.path.isfile(args.toa_transcriptome_relationship_file):
xlib.Message.print(
'error',
f'*** The file {args.toa_transcriptome_relationship_file} 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)
# 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 "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 "dataset_id"
if args.dataset_id is None:
xlib.Message.print(
'error',
'*** The dataset identification is not indicated in the input arguments.'
)
OK = False
else:
args.dataset_id = args.dataset_id.lower()
# check "species_id"
if args.species_id is None:
xlib.Message.print(
'error',
'*** The species identification is not indicated in the input arguments.'
)
OK = False
else:
args.species_id = args.species_id.lower()
# check "gene_desc_dir"
if args.gene_desc_dir is None:
xlib.Message.print(
'error',
'*** The gene description file directoty is not indicated in the input arguments.'
)
OK = False
elif not os.path.isdir(args.gene_desc_dir):
xlib.Message.print(
'error', f'*** The directory {args.gene_desc_dir} does not exist.')
OK = False
# check "interpro_file"
if args.interpro_file is None:
xlib.Message.print(
'error',
'*** The InterPro file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.interpro_file):
xlib.Message.print(
'error', f'*** The file {args.interpro_file} does not exist.')
OK = False
# check "go_file"
if args.go_file is None:
xlib.Message.print(
'error',
'*** The Gene Ontology file is not indicated in the input arguments.'
)
OK = False
elif not os.path.isfile(args.go_file):
xlib.Message.print('error',
f'*** The file {args.go_file} does not exist.')
OK = False
# check "mapman_file"
if args.mapman_file is None:
xlib.Message.print(
'error',
'*** The MapMan file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.mapman_file):
xlib.Message.print('error',
f'*** The file {args.mapman_file} 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)
# 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 "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 "dataset_id"
if args.dataset_id is None:
xlib.Message.print(
'error',
'*** The dataset identification is not indicated in the input arguments.'
)
OK = False
else:
args.dataset_id = args.dataset_id.lower()
# check "blast_file_format"
if args.blast_file_format is None:
xlib.Message.print(
'error',
'*** The BLAST file format is not indicated in the input arguments.'
)
OK = False
elif not xlib.check_code(args.blast_file_format,
xlib.get_blast_file_format_code_list(),
case_sensitive=False):
xlib.Message.print(
'error',
f'*** The BLAST file format has to be {xlib.get_blast_file_format_code_list_text()}.'
)
OK = False
# check "blast_file"
if args.blast_file is None:
xlib.Message.print(
'error',
'*** The BLAST file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.blast_file):
xlib.Message.print('error',
f'*** The file {args.blast_file} 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)
# 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 "xml_file_list"
if args.xml_file_list is None:
xlib.Message.print(
'error',
'*** The list of XML file paths is not indicated in the input arguments.'
)
OK = False
else:
# initialize the XML file list
xml_file_list = []
# split "xml_file_list" in a string values list
xml_file_list = args.xml_file_list.split(',')
# check if XML file exist
for i in range(len(xml_file_list)):
xml_file_list[i] = xml_file_list[i].strip()
if not os.path.isfile(xml_file_list[i]):
xlib.Message.print(
'error',
f'*** The file {xml_file_list[i].strip()} does not exist.')
OK = False
# set the argument value
args.xml_file_list = xml_file_list
# check "toa_transcriptome_relationship_file"
if args.toa_transcriptome_relationship_file is None:
args.toa_transcriptome_relationship_file = 'NONE'
elif args.toa_transcriptome_relationship_file.upper() == 'NONE':
args.toa_transcriptome_relationship_file = args.toa_transcriptome_relationship_file.upper(
)
elif not os.path.isfile(args.toa_transcriptome_relationship_file):
xlib.Message.print(
'error',
f'*** The file {args.toa_transcriptome_relationship_file} does not exist.'
)
OK = False
# check "toa_transdecoder_relationship_file"
if args.toa_transdecoder_relationship_file is None:
args.toa_transdecoder_relationship_file = 'NONE'
elif args.toa_transdecoder_relationship_file.upper() == 'NONE':
args.toa_transdecoder_relationship_file = args.toa_transdecoder_relationship_file.upper(
)
elif args.toa_transdecoder_relationship_file.upper(
) != 'NONE' and args.toa_transcriptome_relationship_file.upper() == 'NONE':
xlib.Message.print(
'error',
'*** The TOA-TransDecoder identification relationships file has to be NONE when TOA-transcriptome identification relationships file is NONE.'
)
OK = False
elif not os.path.isfile(args.toa_transdecoder_relationship_file):
xlib.Message.print(
'error',
f'*** The file {args.toa_transdecoder_relationship_file} does not exist.'
)
OK = False
# check "merged_file"
if args.merged_file is None:
xlib.Message.print(
'error',
'*** The merged 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 "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 "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 "ontology_file"
if args.ontology_file is None:
xlib.Message.print(
'error',
'*** The ontology file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.ontology_file):
xlib.Message.print(
'error', f'*** The file {args.ontology_file} does not exist.')
OK = False
# check "ec2go_file"
if args.ec2go_file is None:
xlib.Message.print(
'error',
'*** The ec2go file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.ec2go_file):
xlib.Message.print('error',
f'*** The file {args.ec2go_file} does not exist.')
OK = False
# check "kegg2go_file"
if args.kegg2go_file is None:
xlib.Message.print(
'error',
'*** The kegg2go file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.kegg2go_file):
xlib.Message.print(
'error', f'*** The file {args.kegg2go_file} does not exist.')
OK = False
# check "metacyc2go_file"
if args.metacyc2go_file is None:
xlib.Message.print(
'error',
'*** The metacyc2go file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.metacyc2go_file):
xlib.Message.print(
'error', f'*** The file {args.metacyc2go_file} does not exist.')
OK = False
# check "interpro2go_file"
if args.interpro2go_file is None:
xlib.Message.print(
'error',
'*** The interpro2go file is not indicated in the input arguments.'
)
OK = False
elif not os.path.isfile(args.interpro2go_file):
xlib.Message.print(
'error', f'*** The file {args.interpro2go_file} 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)
# 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 "annotation_file_1"
if args.annotation_file_1 is None:
xlib.Message.print('error', '*** The first annotation file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.annotation_file_1):
xlib.Message.print('error', f'*** The file {args.annotation_file_1} does not exist.')
OK = False
# check "type_1"
if args.type_1 is None:
xlib.Message.print('error', '*** The type of first annotation file is not indicated in the input arguments.')
OK = False
elif not xlib.check_code(args.type_1, 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_1 = args.type_1.upper()
# check "annotation_file_2"
if args.annotation_file_2 is None:
xlib.Message.print('error', '*** The second annotation file is not indicated in the input arguments.')
OK = False
elif args.annotation_file_2.upper() == 'NONE':
args.annotation_file_2 = args.annotation_file_2.upper()
elif not os.path.isfile(args.annotation_file_2):
xlib.Message.print('error', f'*** The file {args.annotation_file_2} does not exist.')
OK = False
# check "type_2"
if args.type_2 is None:
xlib.Message.print('error', '*** The format of second annotation file is not indicated in the input arguments.')
OK = False
elif args.type_2.upper() == 'NONE' and args.annotation_file_2 != 'NONE':
xlib.Message.print('error', '*** The format of second annotation file has to be NONE if the second annotation file is NONE')
OK = False
elif args.type_2.upper() == 'NONE' and args.annotation_file_2 == 'NONE':
args.type_2 = args.type_2.upper()
elif not xlib.check_code(args.type_2, 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_2 = args.type_2.upper()
# check "merger_file"
if args.merger_file is None:
xlib.Message.print('error', '*** The merged file is not indicated in the input arguments.')
OK = False
# check "merger_operation"
if args.merger_operation is None:
xlib.Message.print('error', '*** The merger operation is not indicated in the input arguments.')
OK = False
elif args.merger_operation.upper() == 'SAVE1' and args.annotation_file_2 != 'NONE':
xlib.Message.print('error', '*** The merger operation SAVE1 is only valid when the second annotation file is NONE.')
OK = False
elif args.merger_operation.upper() != 'SAVE1' and not xlib.check_code(args.merger_operation, xlib.get_annotation_merger_operation_code_list(), case_sensitive=False) :
xlib.Message.print('error', f'*** The merger operation has to be {xlib.get_annotation_merger_operation_code_list_text()}.')
OK = False
else:
args.merger_operation = args.merger_operation.upper()
# check "header"
if args.header is None:
args.header = xlib.Const.DEFAULT_HEADER
elif not xlib.check_code(args.header, xlib.get_header_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** header has to be {xlib.get_header_code_list_text()}.')
OK = False
else:
args.header = args.header.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)
# 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 "phase_dir"
if args.phase_dir is None:
xlib.Message.print('error', '*** The PHASE file directory is not indicated in the input arguments.')
OK = False
elif not os.path.isdir(args.phase_dir):
xlib.Message.print('error', f'*** The directory {args.phase_dir} does not exist.')
OK = False
# check "phase_extension"
if args.phase_extension is None:
xlib.Message.print('error', '*** The extension of PHASE files is not indicated in the input arguments.')
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 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 "structure_file"
if args.structure_file is None:
xlib.Message.print('error', '*** The converted Structure 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):
'''
Verity the input arguments.
'''
# initialize the control variable
OK = True
# check loci_file_path
if args.loci_file_path is None:
xlib.Message.print(
'error',
'*** A loci file path is not indicated in the input arguments.')
OK = False
else:
if not os.path.isfile(args.loci_file_path):
xlib.Message.print(
'error', f'*** The file {args.loci_file_path} does not exist.')
OK = False
if not args.loci_file_path.endswith('.loci'):
xlib.Message.print(
'error',
f'*** The file {args.loci_file_path} does not end in ".loci".')
OK = False
# check stats_file_path
if args.stats_file_path is None:
xlib.Message.print(
'error',
'*** A statistics path is not indicated in the input arguments.')
OK = False
else:
if not args.stats_file_path.endswith('.csv'):
xlib.Message.print(
'error',
f'*** The file {args.stats_file_path} does not end in ".csv".')
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 "input_file"
if args.input_file is None:
xlib.Message.print('error', '*** The input file is not indicated in the input arguments.')
OK = False
elif not os.path.isfile(args.input_file):
xlib.Message.print('error', f'*** The file {args.input_file} does not exist.')
OK = False
# check "file_format"
if args.file_format is None:
xlib.Message.print('error', '*** The merger operation is not indicated in the input arguments.')
OK = False
elif not xlib.check_code(args.file_format, xlib.get_restored_file_format_code_list(), case_sensitive=False):
xlib.Message.print('error', f'*** The merger operation has to be {xlib.get_restored_file_format_code_list_text()}.')
OK = False
else:
args.file_format = args.file_format.upper()
# check "toa_transcriptome_relationship_file"
if args.toa_transcriptome_relationship_file is None:
xlib.Message.print('error', '*** The file with TOA-transcriptome identification relationships.')
OK = False
elif not os.path.isfile(args.toa_transcriptome_relationship_file):
xlib.Message.print('error', f'*** The file {args.toa_transcriptome_relationship_file} does not exist.')
OK = False
# check "toa_transdecoder_relationship_file"
if args.toa_transdecoder_relationship_file is None:
xlib.Message.print('error', '*** The file path with TOA-TransDecoder identification relationships.')
elif args.toa_transdecoder_relationship_file.upper() == 'NONE':
args.toa_transdecoder_relationship_file = args.toa_transdecoder_relationship_file.upper()
elif not os.path.isfile(args.toa_transdecoder_relationship_file):
xlib.Message.print('error', f'*** The file {args.toa_transdecoder_relationship_file} does not exist.')
OK = False
# check "output_file"
if args.output_file is None:
xlib.Message.print('error', '*** The output 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')
