#!/usr/bin/python
import numpy

#INPUT
#list of chromosome lengths - ordered 
#shift, an integer
#chrom and pos for the locus that should be shifted, chrom is a str of the form '1' or 'Chr1' or 'chr1' and pos is an integer
#returns new chrom and pos
def circular_rand(chrom, pos, shift, chr_lengths):
    genome_size = sum(chr_lengths)
    genome_cumsum = list(numpy.cumsum(chr_lengths))
    #genome_offset is [0, chr1len, chr1+chr2len, ..., genome_len]
    genome_offset = genome_cumsum[:]
    genome_offset.insert(0, 0)
    genome_offset_dict = {str(i): genome_offset[i-1] for i in range(1, len(chr_lengths)+1)}
    prefix = ''
    if 'chr' in chrom.lower():
        chrom = chrom[3:]
        prefix = chrom[0:3]
    genomic_coord = pos + genome_offset_dict[chrom]
    ###circular randomisation
    rand_genomic_coord = (genomic_coord + shift) % genome_size
    #decompose into chrom and pos
    for c, offset in enumerate(genome_offset):
        if rand_genomic_coord - offset <= chr_lengths[c]:
            new_chrom = prefix + str(c+1)
            new_pos = rand_genomic_coord - offset
            break
    return [new_chrom, new_pos]