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How to use psmap method in fMBT

Best Python code snippet using fMBT_python

psmap.py

Source:psmap.py

...9        return fib(n-1) + fib(n-2)10print "map..."11print map(fib, [32] * 16)12print "psmap..."13print psmap.psmap(fib, [32] * 16)14---152. Example, use all workers registered on two pythonshare-server hubs:16import psmap17psmap.use_workers(hub_1_hostspec)18psmap.use_workers(hub_2_hostspec)19...20psmap.psmap(fib, [32] * 16)21---223. Example, use explicitly listed workers, some may be local, some remote:23import psmap24psmap.use_worker(worker_1_hostspec)25psmap.use_worker(worker_2_hostspec)26...27psmap.use_worker(worker_n_hostspec)28psmap.psmap(fib, [32] * 16)29"""30import atexit31import Queue32import inspect33import os34import pythonshare35import subprocess36import thread37import time38g_hubs = []39g_hubs_kill_at_exit = []40g_workers = []41g_worker_conns = []42g_workers_free = Queue.Queue()43def soe(cmd, stdin="", cwd=None, env=None, bg=False):44    """Run cmd, return (status, stdout, stderr)"""45    run_env = dict(os.environ)46    if not env is None:47        run_env.update(env)48    try:49        p = subprocess.Popen(50            cmd,51            stdin=subprocess.PIPE,52            stdout=subprocess.PIPE,53            stderr=subprocess.PIPE,54            close_fds=True,55            cwd=cwd,56            env=run_env)57        if bg:58            return (p, None, None)59        out, err = p.communicate(input=stdin)60    except Exception, e:61        return (None, None, str(e))62    return (p.returncode, out, err)63def use_workers(hub_hostspec):64    g_hubs.append(hub_hostspec)65    conn = pythonshare.connect(hub_hostspec)66    for ns in conn.ls_remote():67        use_worker(hub_hostspec + "/" + ns)68def launch_workers(count, hub_port=9999):69    hub_addr = launch_hub(hub_port)70    for worker_id in xrange(count):71        launch_worker(worker_id, hub_addr)72def launch_hub(port=9999):73    hub_addr = "localhost:%s" % (port,)74    try:75        pythonshare.connect(hub_addr).kill_server()76    except:77        pass78    soe(["pythonshare-server", "-p", hub_addr.split(":")[-1]])79    g_hubs_kill_at_exit.append(hub_addr)80    g_hubs.append(hub_addr)81    return hub_addr82def launch_worker(worker_id, hub_addr):83    if hub_addr is None:84        hub_addr = g_hub_addr85    namespace = str(worker_id)86    soe(["pythonshare-server", "-p", "stdin", "-n", namespace, "-E", hub_addr],87        bg=True)88    worker_addr = hub_addr + "/" + namespace89    use_worker(worker_addr)90def use_worker(worker_hostspec):91    conn = pythonshare.connect(worker_hostspec)92    g_workers.append(worker_hostspec)93    g_worker_conns.append(conn)94    g_workers_free.put(conn)95    thread.start_new_thread(eval_thread, ())96def _clean_up():97    for _ in xrange(len(g_workers)):98        g_workers_free.put(None)99        eval_jobs.put(None)100        time.sleep(0.01)101    for conn in g_worker_conns:102        try:103            conn.close()104        except:105            pass106    for hub_addr in g_hubs_kill_at_exit:107        try:108            pythonshare.connect(hub_addr).kill_server()109        except:110            pass111atexit.register(_clean_up)112eval_results = Queue.Queue()113eval_jobs = Queue.Queue()114def eval_thread():115    while 1:116        conn = g_workers_free.get()117        if conn is None:118            break119        job = eval_jobs.get()120        if job is None:121            break122        try:123            job['conn'] = conn124            job['result'] = job['conn'].eval_(job['code'])125            eval_results.put(job)126        finally:127            g_workers_free.put(conn)128def psmap(func, params_list):129    func_source = inspect.getsource(func)130    results = [None] * len(params_list)131    for worker_conn in g_worker_conns:132        worker_conn.exec_(func_source)133    for job_index, params in enumerate(params_list):134        if isinstance(params, tuple):135            params_tuple = params136        else:137            params_tuple = (params,)138        eval_jobs.put({139            'conn': None,140            'job_index': job_index,141            'code': func.__name__ + repr(params_tuple)})142    for params in params_list:143        job = eval_results.get()144        results[job['job_index']] = job['result']145    return results146def fib(n):147    if n <= 1:148        return 1149    else:150        return fib(n-1) + fib(n-2)151if __name__ == "__main__":152    import sys153    if len(sys.argv) == 1:154        launch_workers(8)155    else:156        print "using workers from hubs: ", ", ".join(sys.argv[1:])157        for hub in sys.argv[1:]:158            use_workers(hub)159    print "running", len(g_worker_conns), "workers"160    job_count = 30161    print "will run", job_count, "jobs"162    print "running local map..."163    s = time.time()164    print map(fib, [31] * job_count)165    e = time.time()166    print "map:", e-s167    print "running psmap..."168    s = time.time()169    print psmap(fib, [31] * job_count)170    e = time.time()...

pseudo2refConvert.py

Source:pseudo2refConvert.py

1import sys2def gapFlanks(ch,pos,psmap,FR):3    for i in range(int(pos)-4,int(pos)+5):4        if psmap[ch][i+1] - psmap[ch][i] > 1:5            if FR == "F":6                return psmap[ch][i]7            else:8                return psmap[ch][i+1]9    print "Error: no gap found", psmap[ch][int(pos)-4], psmap[ch][int(pos)+5]10    sys.exit()11def isGap(ch,pos,psmap):12    """if there is a gap near the position to be transformed13    return the left most position of the gap for a forward read and the rightmost for a reverse read14    else, return the normal transformation of the position"""15    if int(pos)+5 >= len(psmap[ch]) or int(pos)-4 < 0:16        return 017    elif abs(psmap[ch][int(pos)+5] - psmap[ch][int(pos)-4]) > 10:18        return 119    else:20        return 021def pseudo2refConvert_portal(bedFILE,pseudo2refMap,outFILE):22    pseudoMap=pseudo2refMap23    print "Converting coordinates from pseudospace to reference-based coordinates..."24    with open(bedFILE, 'r') as fIN, open(outFILE, 'w') as fOUT:25        line_ct=126        for line in fIN:27            orgls=line.split()28            ls=orgls[:-3]+orgls[-1:]29            chrom=ls[0]30            for ch in pseudoMap:31                if ch == chrom:32                    if ls[1].isdigit() and not ls[2].isdigit():33                        if isGap(chrom,ls[1],pseudoMap) == 0:34                            ls[1]=pseudoMap[chrom][int(ls[1])-1]35                        else:36                            ls[1]=gapFlanks(chrom,ls[1],pseudoMap,"F")37                    elif not ls[1].isdigit() and ls[2].isdigit():38                        if isGap(chrom,ls[2],pseudoMap) == 0:39                            ls[2]=pseudoMap[chrom][int(ls[2])]40                        else:41                            ls[2]=gapFlanks(chrom,ls[2],pseudoMap,"R")42                    elif ls[1].isdigit() and ls[2].isdigit():43                        if isGap(chrom,ls[1],pseudoMap) == 0:44                            ls[1]=pseudoMap[chrom][int(ls[1])-1]45                        else:46                            ls[1]=gapFlanks(chrom,ls[1],pseudoMap,"F")47                        if isGap(chrom,ls[2],pseudoMap) == 0:48                            ls[2]=pseudoMap[chrom][int(ls[2])]49                        else:50                            ls[2]=gapFlanks(chrom,ls[2],pseudoMap,"R")51                    if line_ct<10:52                        line_ct="0"+str(line_ct)53                    fOUT.write("\t".join([str(x) for x in ls])+"\tte"+str(line_ct)+"\n")54                    line_ct=int(line_ct)...

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