Source code for iCallSV.checkparameters

"""
checkparameters
~~~~~~~~~~~~~~~

:Description: This modules checks the parameters for various type of inputs.

"""
'''
Created on Mar 16, 2015
Description: This modules checks the parameters for various type of inputs.
@author: Ronak H Shah
'''

import os
import sys
import logging
import coloredlogs

# initiate Logger
logger = logging.getLogger('iCallSV.checkparameters')
coloredlogs.install(level='DEBUG')
# Check if the file exist


[docs]def checkFile(fileToCheck): """ Check `if the file exists or not`` :param str fileToCheck: Name of the file to be checked. :return: None :rtype: None """ if(os.path.isfile(fileToCheck)): logger.info("checkparameters:Given File: %s exists.", fileToCheck) else: logger.fatal( "checkparameters:Given File: %s does not exists. Sorry please check this Input and Run Again.", fileToCheck) sys.exit(1)
# Check if the Directory exists
[docs]def checkDir(folderToCheck): """ Check `if the folder exists or not`` :class:`str`. :param str folderToCheck: Name of the folder to be checked. :return: None :rtype: None """ if(os.path.isdir(folderToCheck)): logger.info("checkparameters:Given Directory: %s exists.", folderToCheck) else: logger.fatal( "checkparameters:Given Directory: %s does not exists. Sorry please check this Input and Run Again.", folderToCheck) sys.exit(1)
# Check if the variable is and Integer
[docs]def checkInt(variableToCheck, variableName): """ Check `if the variable is int or not`` :param int variableToCheck: Check if it is int or not :param str variableName: Name of the int object to be verified :return: None :rtype: None """ if(isinstance(variableToCheck, int)): logger.info( "checkparameters: %s Variable: %d is an Integer.", variableName, variableToCheck) else: logger.fatal( "checkparameters: %s Variable: %d is not an Integer. Sorry please check this Input and Run Again.", variableName, variableToCheck) sys.exit(1)
# Check if the given variable is not Empty
[docs]def checkEmpty(variableToCheck, variableName): """ Check `if the variable is None or not`` :param str variableToCheck: check if str is None or not :param str variableName: Name of the None object to be verified :return: None :rtype: None """ if(variableToCheck): logger.info("checkparameters: %s Variable:%s is not empty.", variableName, variableToCheck) else: logger.fatal( "checkparameters: %s Variable:%s is empty. Sorry please check this Input and Run Again.", variableName, variableToCheck) sys.exit(1)
# Check the Delly Analysis Type is Valid or Not
[docs]def checkDellyAnalysisType(varaibleToCheck): """ Check `if the variable for Delly analysis exists or not`` :param str variableToCheck: check if str is DEL|DUP|INV|TRA :return: None :rtype: None """ if(varaibleToCheck == "DEL" or varaibleToCheck == "DUP" or varaibleToCheck == "INV" or varaibleToCheck == "TRA"): logger.info("checkparameters:Given Delly Analysis Type:%s is valid.", varaibleToCheck) else: logger.fatal( "checkparameters:Given Delly Analysis Type: %s is not valid. Sorry please check this Input and Run Again.", varaibleToCheck) sys.exit(1)