contemp.py

# coding: utf8
import pyopencl as cl, numpy as np, os, sys, re
from functools import reduce

class ListCounter(dict):
    def __missing__(self, key):
        self[key] = []
        return self[key]

def get_device():
    devs = []
    for pf in cl.get_platforms():
        for dev in pf.get_devices():
            devs.append(dev)

    if len(devs) == 0:
        sys.exit(1)

    devs = sorted(devs, key = lambda dev: repr(dev.get_info(di.TYPE))
            + repr(dev.get_info(di.LOCAL_MEM_TYPE) % 2) 
            + repr(dev.get_info(di.MAX_COMPUTE_UNITS))
            + repr(dev.get_info(di.LOCAL_MEM_SIZE)), reverse=True)
    return devs[0]

def count_vars_ocl(f, f_size, pattern_size_min, pattern_size_max):
    di = cl.device_info
    mf = cl.mem_flags
    dt = np.dtype('u1')
    fArr = np.fromfile(f, dt, f_size)
    charGetTpl = open('char_get.cl.tpl').readline()
    countTpl = open('pattern_count.cl').read()

    dev = get_device()
    ctx = cl.Context(devices=[dev])
    fBuf = cl.Buffer(ctx, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf = fArr)
    prog = cl.Program()

    for i in range(pattern_size_min, pattern_size_max + 1):
        charGetLines = ''
        for j in range(f_size):
            charGetLines += charGetTpl
        resArr = np.zeros(f_size)

    return counts

def count_vars(f, f_size, pattern_size_min, pattern_size_max):
    counts = ListCounter()
    for i in range(pattern_size_min, pattern_size_max + 1):
        f.seek(0)
        a = f.read(i)
        counts[a].append(0)

        for j in range(1, f_size - i + 1):
            a = a[1:] + f.read(1)
            counts[a].append(j)
    return counts

if __name__ == '__main__':

    fn = 'dna.seq'
    f = open(fn)
    pattern_size_min = 50
    pattern_size_max = 50

    f_size = os.path.getsize(fn)
    if len(sys.argv) > 1 and re.match('^\d*[1-9]\d*$', sys.argv[1]):
            f_size = min(int(sys.argv[1]), f_size)

    print_all = len(sys.argv) > 2 and sys.argv[2] == 'list'

    variations = reduce(lambda x,y: x + 4**y, [0] + list(range(pattern_size_min, pattern_size_max + 1)))
    counts = count_vars(f, f_size, pattern_size_min, pattern_size_max)
    if print_all:
        for k in sorted(counts.keys(), key = lambda key: repr(len(key)) + key):
            print(k + ':' + repr(len(counts[k])))
    print('Variations: ' + repr(len(counts)) + ' out of ' + repr(variations) + ' (' + repr(f_size - 1) + ' possible in given string length)')