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extension100.py
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extension100.py
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from os import path
from futils import timeit, read_json
from pprint import pprint
import json
LYCOPENE = True
TEMPLATE_DIR = "/data/Imperial/src/matching/templates/"
TEMPLATE_FILE = "template_lycopene_sanger.json"
TEMPLATE = path.join(TEMPLATE_DIR, TEMPLATE_FILE)
RES_DIR = "/data/Imperial/src/matching/output_results/"
MAT_2 = "20210807-231259-matching-results-run_cm2_2-cm2-lycopene-1target-UTR1-RBS-A12-UTR2-RBS-A12-UTR3-RBS-A12-CrtI-th05-run-1-from-1.json"
REC_2 = "20210807-231259-reconstruction-run_cm2_2-cm2-lycopene-1target-UTR1-RBS-A12-UTR2-RBS-A12-UTR3-RBS-A12-CrtI-th05-run-1-from-1.json"
REC_2 = "20210812-111500-reconstruction-run_cm2_2-cm2-lycopene-100targets-sanger-th09-run-1-from-1.json"
MATCHES_2 = path.join(RES_DIR, MAT_2)
RECS_2 = path.join(RES_DIR, REC_2)
@timeit
def reconstruct_slices(rec, template, targets):
"""
Extend
targets = [
{
"name":"TargetABC",
"slices": {
"revE": "BASIC_construct_UTR1-RBS-A12-UTR2-RBS-A12-UTR3-RBS-A12_CrtE_01.seq",
"revI": "BASIC_construct_UTR1-RBS-A12-UTR2-RBS-A12-UTR3-RBS-A12_CrtI_01.seq",
"revB": "BASIC_construct_UTR1-RBS-A12-UTR2-RBS-A12-UTR3-RBS-A12_CrtB_01.seq"
}
},
...
]
"""
template_size = len(template["template"]["structure"])
template_slices = template["template_slices"]
dd = {}
l = []
for slice in rec:
print(slice)
ll = []
for ss in slice:
d = {}
sp = ss["path"]
# Filter dict with wanted keys only 'name' and 'score'
tr = [{k: d[k] for k in ["name", "score"]} for d in sp]
ex = extend_slice(ss["slice"], template_slices, template_size, tr)
slice_name = ss["slice_name"]
d[slice_name] = ex
d["score"] = ss["score"]
d["name"] = slice_name
ll.append(d)
best = sorted(ll, key=lambda d: d["score"])
# check if list is not empty
if best:
l.append(best[-1])
print("Best:", l)
r = addition(l, template_size)
return r
def addition(es, template_size):
"""
Addition
"""
# TODO Change this, no hardcode
target_json_file = (
"/data/Imperial/src/matching/targets/target_lycopene_sanger_10.json"
)
with open(target_json_file) as json_file:
target = json.load(json_file)
targets = target["targets"]
print("/" * 80)
pprint(es)
print("/" * 80)
u = []
for target in targets:
li = []
for k, v in target["slices"].items():
print(k, v)
v = path.basename(v)
bn = v.split(".")[0]
li.append(bn)
print("Li:", li)
addi = []
for col in range(template_size):
print("Part:", col + 1)
l = []
for k, v in enumerate(li):
print("Slice:", k, v)
a = []
for i in es:
print("Name:", i["name"])
if v == i["name"]:
print("Match")
print(i[i["name"]])
a = i[i["name"]]
if a:
l.append(a[col])
print("L", l)
cand = sorted(l, key=lambda k: k["score"])
if cand:
print(cand)
print("-" * 80)
addi.append(cand[-1])
u.append({target["name"]: addi})
return u
def extend_slice(slice_name, slices, template_size, target_result):
"""
Extend slice
"""
ext_obj = {"name": "Empty", "score": 0.0}
extended_list = [ext_obj] * template_size
el = extended_list
for slice in slices:
if slice["name"] == slice_name:
print("Slice:", slice_name)
for i, n in enumerate(
slice["template_slice"]
): # "template_slice":[1, 2, 3, 4]
pos = n - 1
el = el[:pos] + [target_result[i]] + el[pos + 1 :]
return el
def main():
"""
Main
"""
rec = read_json(RECS_2)
template = read_json(TEMPLATE)
# target_json_file = "/data/Imperial/src/matching/targets/target_lycopene_1.json"
target_json_file = (
"/data/Imperial/src/matching/targets/target_lycopene_sanger_A.json"
)
with open(target_json_file) as json_file:
target = json.load(json_file)
targets = target["targets"]
r = reconstruct_slices(rec, template, targets)
print("Construct: ", r)
pprint(r)
if __name__ == "__main__":
main()