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main.py
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import json
import pprint
from collections import defaultdict
import simulate as s
pp = pprint.PrettyPrinter(indent=4)
def simulate_simple_excisions(chrlen, chrranges):
"""
Simulate simple excision.
"""
conf = {s.N: 1,
s.NEIGHBOR: True,
s.SINGLE_CHR: True,
s.MIN_TANDEM_DUPLICATION: 1000,
s.WEIGHT_CHR: [50] * len(chrlen),
s.P_DEL_LEFT: 0,
s.P_DEL_RIGHT: 0,
s.P_INVERT: 0,
s.P_DUP: 0,
s.P_FOLDBACK: 0,
s.P_RETURN: 0,
s.P_CHOOSE_RANDOM: 1
}
for i in range(0, 5):
ecDNAdict = defaultdict(int)
file = """sim_2/excision/circ_1_{}.bed""".format(str(i))
# print(file)
for j in range(0, conf[s.N]):
ecDNA, cov = s.simulation(chrlen, chrranges, conf, type="random")
ecDNAdict[j] = {}
ecDNAdict[j]["structure"] = ecDNA
ecDNAdict[j]["coverage"] = cov
s.ecDNA2bed(ecDNAdict, file)
def simulate_simple_deletions(chrlen, chrranges):
"""
Simulate simple events like small deletions
"""
conf = {s.N: 2,
s.NEIGHBOR: True,
s.SINGLE_CHR: True,
s.MIN_TANDEM_DUPLICATION: 1000,
s.WEIGHT_CHR: [50] * len(chrlen),
s.P_DEL_LEFT: 60,
s.P_DEL_RIGHT: 60,
s.P_INVERT: 0,
s.P_DUP: 0,
s.P_FOLDBACK: 0,
s.P_RETURN: 0,
s.P_CHOOSE_RANDOM: 1
}
# define number of fragments
for k in range(2, 10):
conf[s.N] = k
# simulation number
for i in [1, 2, 3]:
ecDNAdict = defaultdict(int)
# how many ecDNA per file
for j in range(0, 1):
ecDNA, cov = s.simulation(chrlen, chrranges, conf, type="nonrandom")
ecDNAdict[j] = {}
ecDNAdict[j]["structure"] = ecDNA
ecDNAdict[j]["coverage"] = cov
s.ecDNA2bed(ecDNAdict, """sim_2/simple_del/circ_{}_{}.bed""".format(str(k), str(i)))
def simulate_simple_inversion(chrlen, chrranges):
"""
Simulate simple inversion and deletions
"""
conf = {s.N: 2,
s.NEIGHBOR: True,
s.SINGLE_CHR: True,
s.MIN_TANDEM_DUPLICATION: 1000,
s.WEIGHT_CHR: [50] * len(chrlen),
s.P_DEL_LEFT: 0,
s.P_DEL_RIGHT: 0,
s.P_INVERT: 40,
s.P_DUP: 0,
s.P_FOLDBACK: 0,
s.P_RETURN: 0,
s.P_CHOOSE_RANDOM: 1
}
# define number of fragments
for k in range(2, 10):
conf[s.N] = k
# simulation number
for i in [1, 2, 3]:
ecDNAdict = defaultdict(int)
# how many ecDNA per file
for j in range(0, 1):
ecDNA, cov = s.simulation(chrlen, chrranges, conf, type="nonrandom")
ecDNAdict[j] = {}
ecDNAdict[j]["structure"] = ecDNA
ecDNAdict[j]["coverage"] = cov
s.ecDNA2bed(ecDNAdict, """sim_2/simple_inv/circ_{}_{}.bed""".format(str(k), str(i)))
def simulate_intrachrom_multi_region_random(chrlen, chrranges):
"""
Simulate intrachrom multi region
"""
conf = {s.NEIGHBOR: False,
s.SINGLE_CHR: True,
s.MIN_TANDEM_DUPLICATION: 1000,
s.WEIGHT_CHR: [50] * len(chrlen),
s.P_DEL_LEFT: 60,
s.P_DEL_RIGHT: 60,
s.P_INVERT: 40,
s.P_DUP: 0,
s.P_FOLDBACK: 0,
s.P_RETURN: 0,
# related to foldback
s.P_CHOOSE_RANDOM: 1
}
# define number of fragments
for k in range(2, 10):
conf[s.N] = k
# simulation number
for i in [1, 2, 3]:
ecDNAdict = defaultdict(int)
# how many ecDNA per file
for j in range(0, 1):
ecDNA, cov = s.simulation(chrlen, chrranges, conf, type="random")
ecDNAdict[j] = {}
ecDNAdict[j]["structure"] = ecDNA
ecDNAdict[j]["coverage"] = cov
s.ecDNA2bed(ecDNAdict, """sim_2/intrachrom_random/circ_{}_{}.bed""".format(str(k), str(i)))
def simulate_intrachrom_multi_region_pseudorandom(chrlen, chrranges):
"""
Simulate intrachrom multi region
"""
conf = {s.NEIGHBOR: False,
s.SINGLE_CHR: True,
s.MIN_TANDEM_DUPLICATION: 1000,
s.WEIGHT_CHR: [50] * len(chrlen),
s.P_DEL_LEFT: 60,
s.P_DEL_RIGHT: 60,
s.P_INVERT: 40,
s.P_DUP: 0,
s.P_FOLDBACK: 0,
s.P_RETURN: 0,
# related to foldbacks
s.P_CHOOSE_RANDOM: 1
}
# define number of fragments
for k in range(2, 10):
conf[s.N] = k
# simulation number
for i in [1, 2, 3]:
ecDNAdict = defaultdict(int)
# how many ecDNA per file
for j in range(0, 1):
ecDNA, cov = s.simulation(chrlen, chrranges, conf, type="pseudorandom")
ecDNAdict[j] = {}
ecDNAdict[j]["structure"] = ecDNA
ecDNAdict[j]["coverage"] = cov
s.ecDNA2bed(ecDNAdict, """sim_2/intrachrom/circ_{}_{}.bed""".format(str(k), str(i)))
def simulate_simple_mix(chrlen, chrranges):
"""
Simulate simple inversion and deletions
"""
conf = {s.NEIGHBOR: True,
s.SINGLE_CHR: True,
s.MIN_TANDEM_DUPLICATION: 1000,
s.WEIGHT_CHR: [50] * len(chrlen),
s.P_DEL_LEFT: 60,
s.P_DEL_RIGHT: 60,
s.P_INVERT: 40,
s.P_DUP: 0,
s.P_FOLDBACK: 0,
s.P_RETURN: 0,
# related to foldbacks
s.P_CHOOSE_RANDOM: 1
}
# define number of fragments
for k in range(2, 10):
conf[s.N] = k
# simulation number
for i in [1, 2, 3]:
ecDNAdict = defaultdict(int)
# how many ecDNA per file
for j in range(0, 1):
ecDNA, cov = s.simulation(chrlen, chrranges, conf, type="random")
ecDNAdict[j] = {}
ecDNAdict[j]["structure"] = ecDNA
ecDNAdict[j]["coverage"] = cov
s.ecDNA2bed(ecDNAdict, """sim_2/simple_mix/circ_{}_{}.bed""".format(str(k), str(i)))
def simulate_interchr_multi_regions(chrlen, chrranges):
conf = {s.NEIGHBOR: False,
s.SINGLE_CHR: False,
s.MIN_TANDEM_DUPLICATION: 1000,
s.WEIGHT_CHR: [50] * len(chrlen),
s.P_DEL_LEFT: 60,
s.P_DEL_RIGHT: 60,
s.P_INVERT: 40,
s.P_DUP: 0,
s.P_FOLDBACK: 0,
s.P_RETURN: 0,
# related to foldbacks
s.P_CHOOSE_RANDOM: 1
}
# define number of fragments
for k in range(2, 10):
conf[s.N] = k
# simulation number
for i in [1, 2, 3]:
ecDNAdict = defaultdict(int)
# how many ecDNA per file
for j in range(0, 1):
ecDNA, cov = s.simulation(chrlen, chrranges, conf, type="pseudorandom")
ecDNAdict[j] = {}
ecDNAdict[j]["structure"] = ecDNA
ecDNAdict[j]["coverage"] = cov
s.ecDNA2bed(ecDNAdict, """sim_2/interchrom/circ_{}_{}.bed""".format(str(k), str(i)))
def simulate_foldbacks(chrlen, chrranges):
conf = {s.NEIGHBOR: True,
s.SINGLE_CHR: True,
s.MIN_TANDEM_DUPLICATION: 1000,
s.WEIGHT_CHR: [50] * len(chrlen),
s.P_DEL_LEFT: 60,
s.P_DEL_RIGHT: 60,
s.P_INVERT: 40,
s.P_DUP: 0,
s.P_FOLDBACK: 40,
s.P_RETURN: 0,
# related to foldbacks
s.P_CHOOSE_RANDOM: 10
}
# define number of fragments
for k in range(2, 10):
conf[s.N] = k
# simulation number
for i in [1, 2, 3]:
ecDNAdict = defaultdict(int)
# how many ecDNA per file
for j in range(0, 1):
ecDNA, cov = s.simulation(chrlen, chrranges, conf)
ecDNAdict[j] = {}
ecDNAdict[j]["structure"] = ecDNA
ecDNAdict[j]["coverage"] = cov
s.ecDNA2bed(ecDNAdict, """sim_2/foldback/circ_{}_{}.bed""".format(str(k), str(i)))
def generate_allowed(specify_conformation=None):
if not specify_conformation:
return s.generate_conformation()
else:
return [specify_conformation]
def simulate_structure(chrlen, chrranges, repeat_simulation=5, specify_conformation=[3, 0, 1, 1, 0, 1, 1, 1, 0]):
"""
Args:
chrlen (dict):
chrranges (dict):
accept_criteria (list): topology = {N_FRAG: 0,
FRAG_LEN: 0,
SMALL_DEL: 0,
DUP: 0,
INV: 0,
INTERCHR: 0,
MULTI_REGION: 0,
FOLDBACK: 0,
RETURN: 0
}
"""
allowed_conformations = generate_allowed(specify_conformation)
count = 0
batch = 0
with open("sim_all/summary.txt", "w") as f:
f.write("#sim_id\tbatch_id\tcount_frag\tsmall_del\tdup\tinv\tinterchr\tmulti_region\tfoldback\ttopology\n")
# simulate
for j, accept_criteria in enumerate(allowed_conformations):
conf = {}
conf[s.N] = accept_criteria[s.N_FRAG_POS]
conf[s.FRAG_LEN] = accept_criteria[s.FRAG_LEN_POS]
conf[s.NEIGHBOR] = True if accept_criteria[s.MULTI_REGION_POS] == 0 and accept_criteria[
s.INTERCHR_POS] == 0 else False
conf[s.MIN_TANDEM_DUPLICATION] = 1000
conf[s.WEIGHT_CHR] = [50] * len(chrlen)
conf[s.P_DEL_LEFT] = 0 if accept_criteria[s.SMALL_DEL_POS] == 0 else 30
conf[s.P_DEL_RIGHT] = 0 if accept_criteria[s.SMALL_DEL_POS] == 0 else 30
conf[s.P_DUP] = 0 if accept_criteria[s.DUP_POS] == 0 else 30
conf[s.P_INVERT] = 0 if accept_criteria[s.INV_POS] == 0 else 30
conf[s.P_FOLDBACK] = 0 if accept_criteria[s.FOLDBACK_POS] == 0 else 30
conf[s.P_RETURN] = 0
conf[s.P_CHOOSE_RANDOM] = 100 if accept_criteria[s.FOLDBACK_POS] == 0 and accept_criteria[
s.RETURN_POS] == 0 else 20
conf["chrs_len"] = chrlen
conf["chrs_ranges"] = chrranges
conf["accept_criteria_description"] = "[#frag, len, small_del, dup, inv, interch, multi+region, foldback, return]"
for i in range(0, repeat_simulation):
conf["sim_iteration"] = i
conf["accept_criteria"] = accept_criteria
ecDNA, cov, topology = s.simulation(chrlen, chrranges, conf, acceptance_criteria=accept_criteria)
if ecDNA == None:
# print("Warning! could not find topology", accept_criteria)
pass
else:
ecDNAdict = {}
ecDNAdict["structure"] = ecDNA
ecDNAdict["coverage"] = cov
ecDNAdict["topology"] = topology
metainformation = s.code_metainformation(topology)
count += 1
prefixfile = """sim_all/batch_{}/sim_{}""".format(str(batch), str(count))
f.write("""sim_{}\tbatch_{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n""".format(str(count),
str(batch),
topology[s.N_FRAG],
topology[s.DUP],
topology[s.INV],
topology[s.INTERCHR],
topology[s.MULTI_REGION],
topology[s.FOLDBACK],
metainformation))
s.ecDNA2bed_single(ecDNAdict, prefixfile + ".bed")
with open(prefixfile + ".json", 'w') as g:
json.dump(conf, g)
if count % 100 == 0:
batch += 1
print("#Simulation templates ", count)