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)