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run.py
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executable file
·196 lines (168 loc) · 6.61 KB
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#!/usr/local/bin/python
import os
import shutil
from string import Template
import argparse as ap
import simplejson as js
import random
from copy import deepcopy
import string
import synth
import Queue
import threading
import subprocess
random.seed(124357)
def merge(d1, d2):
d3 = dict()
for (k, v) in d1.items(): d3[k] = v
for (k, v) in d2.items(): d3[k] = v
return d3
def orc(f): #open read close
f = open(f, "r")
ret = f.read()
f.close()
return ret
def package(l, n):
for i in range(0, len(l), n): yield(tuple(l[i:i+n]))
from pprint import *
def prepare_fields_for_sim(data):
cstr = data["constraints"]
defaults = cstr["defaults"]
vol = defaults["volume"]
av = 6.022e23
kD_constraints = cstr["kD"]
for k in data.keys():
if data[k] == None: data[k] = defaults["k_on"]
if type(data[k]) in [str, unicode] and data[k] in defaults: data[k] = defaults[data[k]]
for k_on, k_off, v in kD_constraints:
if k_on in data: data[k_off] = (v * av * vol) * data[k_on]
else:
data[k_on] = defaults["k_on"]
data[k_off] = data[k_on] / (v * 6.022e23 * vol)
pprint(data)
def fix_xtra(xtra):
return dict(package([string.lstrip(s, "-") for s in xtra], 2))
def gen_experiment(data):
constants = data["constants"]
fields = data["fields"]
expr = dict()
todo = []
for (k, v) in fields.items():
typ, val = v["type"], v["value"]
if typ == "constant": expr[k] = val
if typ == "random_uniform":
if isinstance(val, str) and val in constants: val = constants[val]
if len(val) < 3: val.insert(0, "float")
t, lower, upper = val
t = {"float": float, "int": int}[t]
expr[k] = t(random.uniform(lower, upper))
else: todo.append((k, v))
for (k, v) in todo:
typ, val = v["type"], v["value"]
if typ == "Kd_constraint":
field, ratio = val
expr[k] = expr[field]/(ratio * 6.022e23 * constants["volume"])
return expr
def synth_dna(args, xtra):
settings = js.loads(orc(os.path.join("src", "default_synth_dna.json")))
meta = settings["meta"]
data = settings["data"]
if args.descriptor:
loaded = js.loads(orc(args.descriptor))
meta = merge(meta, loaded["meta"])
data = merge(data, loaded["data"])
meta = merge(meta, xtra)
data = merge(meta, data)
if not os.path.exists(meta["temp_dir"]): os.makedirs(meta["temp_dir"])
if not os.path.exists(meta["out_dir"]): os.makedirs(meta["out_dir"])
output = os.path.join(meta["out_dir"], meta["out"])
data["out"] = output
raw = "\n\n".join([synth.gen_strand(data["bp_per_strand"], data["weights"]) for i in range(data["strands"]) ])
with open(output, "w", 0) as f: f.write(raw)
def damage_dna(opts, xtra): pass #TODO
def simulate_dna(opts, xtra):
settings = js.loads(orc(os.path.join("src", "default_simulate_dna.json")))
meta = settings["meta"]
data = settings["data"]
if args.descriptor:
loaded = js.loads(orc(args.descriptor))
meta = merge(meta, loaded["meta"])
data = merge(data, loaded["data"])
meta = merge(meta, xtra)
if args.sanity: meta["sanity"] = True
data = merge(meta, data)
if not os.path.exists(meta["temp_dir"]): os.makedirs(meta["temp_dir"])
if not os.path.exists(meta["out_dir"]): os.makedirs(meta["out_dir"])
output = meta["out"] + ".out"
parsed = os.path.join(meta["temp_dir"], meta["out"] + ".ka")
prepare_fields_for_sim(data)
src = orc(os.path.join("src", "initial.ka")) + "\n" + \
"\n".join([orc(os.path.join("src", s + ".ka")) for s in meta["model"]]) + \
"\n" + orc(os.path.join("src", "observables.ka"))
if "sanity" in meta and meta["sanity"]:
src = src + "\n" + orc(os.path.join("src", "sanity.ka"))
src = Template(src)
with open(parsed, "w", 0) as f:
f.write(src.safe_substitute(data))
print ("Running simulation with")
if "time" in meta:
com = "KaSim -i src/sig/dna.ka -i {} -i {} -t {} -p {} -o {} -d {}".format(
parsed, meta["dna_file"], meta["time"], meta["plot_points"], output, meta["out_dir"])
else:
com = "KaSim -i src/sig/dna.ka -i {} -i {} -e {} -p {} -o {} -d {}".format(
parsed, meta["dna_file"], meta["events"], meta["plot_points"], output, meta["out_dir"])
if "seed" in meta: com = com + " -seed {}".format(meta["seed"])
print (com)
os.system(com)
def worker(q):
while True:
item = q.get()
com = "python run.py simulate -descriptor {}".format(item)
print "Running \n{}".format(com)
print threading.active_count()
print threading.current_thread()
subprocess.call(com, shell=True)
q.task_done()
def experiment_dna(args, xtra):
settings = js.loads(orc(args.descriptor))
meta = settings["meta"]
data = settings["data"]
meta = merge(meta, xtra)
data = merge(meta, data)
direct = os.path.join("experiments", meta["experiment_name"])
if not os.path.exists(direct): os.makedirs(direct)
q = Queue.Queue()
for i in range(meta["runs"]):
d = gen_experiment(data)
m = deepcopy(meta)
m["out_dir"] = direct
m["out"] = "{}_{}".format(meta["experiment_name"], i)
s = {"meta": m, "data": d}
descriptor = os.path.join(direct, m["out"]+".json")
q.put(descriptor)
f = open(descriptor, "w", 0)
js.dump(s, f, sort_keys=True, indent=4)
f.close()
for i in range(meta["parallel"]):
t = threading.Thread(target=worker, args=[q])
t.daemon = True
t.start()
q.join()
parser = ap.ArgumentParser(description = "Task runner for DNA BER pathway simulation")
subparsers = parser.add_subparsers(dest = "type")
parser_synth = subparsers.add_parser("synth", help = "synthesis of DNA strands")
parser_damage = subparsers.add_parser("damage", help = "simulate damage of DNA data")
parser_simulate = subparsers.add_parser("simulate", help = "simulate BER pathway")
parser_simulate.add_argument("-sanity", action='store_true', default=False)
parser_experiment = subparsers.add_parser("experiment", help = "generates/runs series of experiments")
for p in [parser_synth, parser_damage, parser_simulate]:
p.add_argument("-descriptor", help = "mode descriptor", default=None)
parser_experiment.add_argument("descriptor", help = "experiment description")
args, xtra = parser.parse_known_args()
xtra = fix_xtra(xtra)
{
"synth": synth_dna,
"damage": damage_dna,
"simulate": simulate_dna,
"experiment": experiment_dna
}[args.type](args, xtra)