Source code for iCallSV.make_analysis_dir

"""
make_analysis_dir
~~~~~~~~~~~~~~~~~

:Description: This module will make directory structure for running analysis

"""
'''
Created on November 19, 2015
Description: This module will make directory structure for running analysis
@author: Ronak H Shah
::Inputs::
args: Arguments passed to iCallSV
'''

import os
import re
import logging


[docs]def makeOutputDir(args, tool): """ This will make the output directory tree. :param Namespace args: Namespace of args to get other variables :return: Multiple objects :rtype: list """ # Get logging settings SampleDirName = args.caseId static_SV_Dir = "StructuralVariantAnalysis" static_tool_Dir = tool AnalysisDir = os.path.join(args.outdir, static_SV_Dir) ToolDir = os.path.join(AnalysisDir, static_tool_Dir) SampleAnalysisDir = os.path.join(ToolDir, SampleDirName) if not os.path.exists (AnalysisDir): try: os.mkdir(AnalysisDir) except OSError: if(args.verbose): logging.warn("make_output_dir:Dir=>%s exists thus we wont be making it", AnalysisDir) pass else: if(args.verbose): logging.warn("make_output_dir:Dir=>%s exists thus we wont be making it", AnalysisDir) pass if not os.path.exists (AnalysisDir): try: os.mkdir(ToolDir) except OSError: if(args.verbose): logging.warn("make_output_dir:Dir=>%s exists thus we wont be making it", ToolDir) pass else: if(args.verbose): logging.warn("make_output_dir:Dir=>%s exists thus we wont be making it", ToolDir) pass if os.path.isdir(SampleAnalysisDir): if(args.verbose): logging.fatal( "make_output_dir:Dir=>%s exists and we wont run the analysis", SampleAnalysisDir) logging.info("make_output_dir:Please delete this directory and rerun the program") tag = False else: try: os.mkdir(SampleAnalysisDir) tag = True except OSError: if(args.verbose): logging.fatal( "make_output_dir:Dir=>%s exists and we wont run the analysis", SampleAnalysisDir) logging.info("make_output_dir:Please delete this directory and rerun the program") tag = False return(tag, SampleAnalysisDir)