def FormatVariant(FileInfo, Type, Ref, Allele, Crc):
"""Format the variant based on the type
Args:
FileInfo (string): In case of error log this info about file
Type (string): (SNV || Deletion || Insertion)
Ref (string): Nucleotide[s] that is/are present in the reference
Allele (string): Nucleotide[s] that is/are present in the allele
Crc (string): Coding Region Change
Returns:
string: Processed and Formatted variant for the Variant Column
"""
try:
if Type == SNP:
return VariantFormat.ProcessSNP(Ref, Allele, Crc)
elif Type == INSERTION:
return VariantFormat.ProcessInsertion(Ref, Allele, Crc)
elif Type == DELETION:
return VariantFormat.ProcessDeletion(Ref, Allele, Crc)
else:
return ""
except ValidationException as crc_error:
# Log here the crc_error message with File info wherever it
# happened
Logger.Warn("{} <> {} <> {}".format(FileInfo, crc_error.message,
crc_error.errors))
return crc_error.errors
config = {}
with open(os.getcwd() + '/configuration/config.jsonc', 'r') as outfile:
config['features'] = {}
config['features']['backend'] = {}
config['features']['frontend'] = {}
config['features']['database'] = {}
config = json.load(outfile)
try:
with open(os.getcwd() + '/appi.json', 'r') as outfile:
config = { **config, **json.load(outfile) }
except:
Logger.Warn('appi.json does not exists')
def GetConfig():
return config
def WriteAppiConfig(conf):
appiConfig = None
with open(config['root-file'], 'r') as appiFile:
appiConfig = json.load(appiFile)
appiConfig = { **appiConfig, **conf }
appiFile.close()
with open(config['root-file'], 'w') as appiFile:
appiFile.write(json.dumps(appiConfig))
