apa.bed.multi

#!/usr/bin/python3

import apa
import sys
import glob
import queue
import threading
import os
import argparse

parser = argparse.ArgumentParser()
parser.add_argument('-type', action="store", dest="type", default="raw") # raw or expression
parser.add_argument('-lib_id', action="store", dest="lib_id", default=None)
parser.add_argument('-poly_id', action="store", dest="poly_id", default=None)
parser.add_argument('-map_id', action="store", dest="map_id", type=int, default=1)
parser.add_argument('-upstream', type=int, action="store", default=None)
parser.add_argument('-downstream', type=int, action="store", default=None)
parser.add_argument('-ip_filter', action="store_true", dest="ip_filter", default=True)
parser.add_argument('-no_ip_filter', action="store_false", dest="ip_filter")
parser.add_argument('-workers', action="store", dest="workers", default=2, type=int)
args = parser.parse_args()

def worker():
    while True:
        task = q.get()
        os.system(task)
        q.task_done()

# get experiments
e_ids = apa.annotation.libs[args.lib_id].experiments.keys()

tasks = []
for e_id in e_ids:
    pars = []
    pars.append("-type %s" % args.type)
    pars.append("-lib_id %s" % args.lib_id)
    pars.append("-force")
    pars.append("-exp %s" % e_id)
    pars.append("-poly_id %s" % args.poly_id)
    pars.append("-map_id %s" % args.map_id)
    pars.append({True:"-ip_filter", False:"-no_ip_filter"}[args.ip_filter])
    if args.upstream!=None:
        pars.append("-upstream %s" % args.upstream)
    if args.downstream!=None:
        pars.append("-downstream %s" % args.downstream)
    tasks.append("apa.bed %s" % " ".join(pars))
    print(tasks[-1]) # print the last added task

num_worker_threads = args.workers
q = queue.Queue()
threads = []

for i in range(num_worker_threads):
    t = threading.Thread(target=worker)
    t.daemon = True
    t.start()
    threads.append(t)

for item in tasks:
    q.put(item)

q.join()