interpolate_maps.py

index1 = 0
index2 = 0
while index1 < len(posin):
    pos = posin[index1]
    rs = rsin[index1]
    if pos == mappos[index2]:
        #the 1000 Genomes site was genotyped as part of the map
        results.append((rs, pos, mapgpos[index2]))
        index1 = index1 + 1
    elif pos < mappos[index2]:
        #current position in interpolation before marker
        if index2 == 0:
            #before the first site in the map (genetic position = 0)
            results.append((rs, pos, mapgpos[index2]))
            index1 = index1 + 1
        else:
            #interpolate
            prevg = mapgpos[index2 - 1]
            prevpos = mappos[index2]
            frac = (float(pos) - float(mappos[index2 - 1]))/ (float(mappos[index2]) - float(mappos[index2 - 1]))
            tmpg = prevg + frac * (mapgpos[index2] - prevg)
            results.append((rs, pos, tmpg))
            index1 = index1 + 1
    elif pos > mappos[index2]:
        #current position in interpolation after marker
        if index2 == len(mappos) - 1:
            #after the last site in the map (genetic position = maximum in map, note could try to extrapolate based 
            # on rate instead)
            results.append((rs, pos, mapgpos[index2]))

            index1 = index1 + 1
        else:
            #increment the marker
            index2 = index2 + 1