microMappingPipeline.py

#!/usr/bin/env python3
import os.path
from os import path
import pysam
import sys

# command line arguments
inputMarkersFlankingGenes = sys.argv[1] # table with mapped flanking ISBPs from genes
outputDir = sys.argv[2] # output directory ...
genomeQuery = sys.argv[3] # fasta file of the v1 genome (must be fai indexed)
genomeTarget = sys.argv[4] # fasta file of the v2 genome (must bie fai indexed)

def main():

	### check for input files and output directory
	checkFile(file=inputMarkersFlankingGenes)
	if ( not checkDir(directory=outputDir) ):
		sys.stdout.write( " Creating output directory %s" % str(outputDir))
		os.mkdir( outputDir, 0o750 )

	#open for reading the reference file

	### read input file containing the flanking IBSP markers for each gene



def checkFile (file):
	if os.path.isfile(file):
		sys.stdout.write(" File %s found\n" % str(file))
	else:
		sys.stderr.write(" ERROR: Cannot find file %s \n" % str(file))
		sys.exit()

def checkDir(directory):
	if os.path.isdir(directory):
		sys.stdout.write(" Directory %s found\n" % str(directory))
	else:
		sys.stderr.write(" ERROR: Cannot find directory %s \n" % str(directory))


if __name__== "__main__":
	main()