SSR_RepeatFilter.py

#!/usr/bin/env python

## Filter out SSR loci that have the same primer sequences as other loci ##
# Keeps the first occurrence and drops any locus after that has the same F or R primers in 1st primer set.

Usage="""RepeatFilter.py INPUT FILE_INDEX"""

import sys

if len(sys.argv) < 2:
	print(Usage)

else:
	InFileName = sys.argv[1] #MISA output
	file_index = sys.argv[2] #e.g. species name
	OutFileName1 = file_index + ".repeat.txt"
	OutFileName2 = file_index + ".misa_SSR.results"  #output

	WriteOutFile = True
	InFile =open(InFileName, 'r')
	
	if WriteOutFile:
		OutFile1 = open(OutFileName1, 'w')
		OutFile2 = open(OutFileName2, 'w')

	
	LineNumber = 0
	
	primerList=[]
	
	for Line in InFile:
		if LineNumber ==0:
			OutFile2.write(Line)
			OutFile1.write(Line)
		else: 
			Line=Line.strip('\n')
			ElementList = Line.split('\t')
			
			scaffoldID = str(ElementList[0])
			SSRnr = str(ElementList[1])
			
			THE_SSR= str(ElementList[3])
		
			primerF1=str(ElementList[7])
			primerR1=str(ElementList[10])
			
			if (primerF1 in primerList) or (primerR1 in primerList):
				OutFile1.write(Line+"\n")
			else:
				primerList.append(primerF1)
				primerList.append(primerR1)
				OutFile2.write(Line+"\n")
				
		LineNumber += 1