#Name: chr_restore_all
#Autor: Marieke Beltman
#Date: 11-03-2015
#Function: reads map files, selects the first column and changes the first column in the selected chromosome (instead of 0), and writes it in a new file. Needed for .map files from PLINK 1.07, because this version of PLINK doesn't recognize other chromosomes than human.

#For every item in chrList, the map file and a new file will be opened and are send to the function restoreChr.
import sys, getopt

outname = sys.argv[1]


def main(outname):
    chrList = ["27", "28", "1A","25LG1", "25LG2","4A", "LGE22","Z"]
    snpChrList ={}
    for i in chrList:
        snpChrList = openchrFile(i,snpChrList)
    #print(snpChrList)
    mapFile= openFile(outname)
    newMapFile= newFile(outname)
    restoreChr(snpChrList,mapFile,newMapFile)

def openFile(outname):
    with open(outname+".map","r") as mapFile:
        best = mapFile.readlines()
    return best

def openchrFile(i,chrom):
    with open("SNPs_per_chr/chr_GT_"+i+".txt","r") as chrFile:
        chrLines = chrFile.readlines()
        for line in chrLines:
            line = line.strip()
            chrom[line]=i
    return chrom

def newFile(outname):
    new = open(outname+"_2.map","w")
    return new

#Every line in the map file is splitted up and the first item of the line is changed in the chromosome, then the line is written to the new file
def restoreChr(snpChrList,mapFile,newMapFile):
    for line in mapFile:
        if line.startswith('0'):
            line = line.strip().split("\t")
            if line[1] in snpChrList.keys():
                line[0]= snpChrList.get(line[1])
                newMapFile.write(("\t".join(line))+"\n")
            elif line[1] not in snpChrList.keys():
                line[0] = 'Un'
                newMapFile.write(("\t".join(line))+"\n")
        else:
            newMapFile.write(line)


main(outname)