BeagleFormat_AMES.py

#formatting for beagle from ames data

#12feb2014
#tyler kent

def double(inputt, output):

    #specify files to open

    infile=open(inputt, "r")
    linelist=infile.readlines()
    outfile=open(output, "w")

    a=0
    for line in linelist:
        #make list of each word in line
        list=str(linelist[a]).split() 
        #add marker & rs# to new line
        newline=list[0]+"\t"+list[1]+"\t"

        x=12
        for i in range(len(list)-12):
            #for each entry from 12 till the end, add 2 copies to newline
            newline=newline+"\t"+list[x]+"\t"+list[x] 
            x+=1
        #write each new line to the output file
        outfile.write((newline)+"\n")
        a+=1

    infile.close()
    outfile.close()

def markers(inputt, inter):
    
     #specify files to open
    infile=open(inputt, "r")
    linelist=infile.readlines()

    outfile=open(inter,"w")

    #add 'I' to first line
    line="I\t"+str(linelist[0])
    outfile.write(line)

    #add 'M' to remaining lines
    x=1
    for i in range(len(linelist)-1):
        line="M\t"+str(linelist[x])
        outfile.write(line)
        x+=1

    infile.close()
    outfile.close()

  
infile=raw_input("File for input (include full path): ")
inter=raw_input("File for intermediate (include full path): ")
outfile=raw_input("File for output (include full path): ")
markers(infile, inter)
double(inter, outfile)