Source code for schicluster.dev.generate_matrix

import numpy as np
from collections import Counter




def generate_matrix(infile, res, genome, dist, outdir, cell):
    fin = open(infile, 'r')
    if res >= 1000000:
        k = str(res / 1000000) + 'mb'
    elif res >= 1000:
        k = str(res / 1000) + 'kb'

    if genome[:2] == 'hg':
        chrom = [str(i + 1) for i in range(22)]
    elif genome[:2] == 'mm':
        chrom = [str(i + 1) for i in range(19)]

    count = Counter()
    for line in fin:
        tmp = line.strip().split('\t')
        tmp[1], tmp[5] = tmp[1][3:], tmp[5][3:]
        if (np.abs(int(tmp[6]) - int(tmp[2])) >= dist) and (tmp[1] == tmp[5]) and (tmp[1] in chrom):
            tmp[2], tmp[6] = int(tmp[2]) // res, int(tmp[6]) // res
            if tmp[2] > tmp[6]:
                tmp[2], tmp[6] = tmp[6], tmp[2]
            if tmp[2] != tmp[6]:
                pos = '-'.join([tmp[1], str(tmp[2]), str(tmp[6])])
                count[pos] += 1

    fin.close()
    fout = {c: open(outdir + 'chr' + c + '/' + cell + '_chr' + c + '.txt', 'w') for c in chrom}
    for key in count:
        tmp = key.split('-')
        fout[tmp[0]].write('{0}\t{1}\t{2}.0\n'.format(tmp[1], tmp[2], count[key]))

    for c in chrom:
        fout[c].close()
    return