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run_cm2_10.py
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run_cm2_10.py
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import json
import logging
from os import path
from pathlib import Path
import time
from reconstruction2 import reconstruct
import fnmatch
from pprint import pprint
from extension10 import reconstruct_slices, addition
from futils import timeit
from tqdm import tqdm
from matching import Library, Sequence, match_library
# Logging configuration
current_file = path.basename(__file__).split(".")[0]
LYCOPENE = True
@timeit
def match_libs(seq, libs, threshold=0.5):
"""
Match libs with the sequence
"""
result = []
for lib in tqdm(libs):
pop = {}
pop["library"] = lib["name"]
# See algo1_lycopene for the parameter below in the template
# threshold = lib["score_threshold"]
candidates = match_library(seq, Library(lib), threshold, direction53=False)
cl = []
for candidate in candidates:
for c in candidate:
cl.append(
{
"name": c.name,
"score": c.score,
"start": c.start,
"length": c.length,
"end": c.end,
}
)
pop["candidates"] = cl
result.append(pop)
return result
def get_slices_libs(template):
"""
Get slices libraries
Args:
template (dict): Template JSON data as a dict structure
Returns:
dict of slices libraries
"""
slices_libs = {}
for sli in template["template_slices"]:
libs = []
for pos in sli["template_slice"]:
lib = template["template"]["structure"][pos - 1]["library_source"]
libs.append(template["component_sources"][lib])
slices_libs[sli["name"]] = libs
return slices_libs
@timeit
def iter_all_seq(
targets_param,
template_json_file,
match_output_filename,
reconstruction_output_filename,
extension_output_filename,
threshold=0.99,
):
"""
Iterate over target sequences
"""
target_json_file = targets_param["file"]
# Get targets from JSON file
with open(target_json_file) as json_file:
target = json.load(json_file)
# Get sequences TU in order of template
with open(template_json_file) as json_file:
template = json.load(json_file)
print("Target:", target)
print("Template:", template)
targets = target["targets"]
slices = template["template_slices"]
print("Slices:", slices)
print("Targets_param:", targets_param)
# Loop over the targets
r = []
order_of_targets_names = []
for target in targets:
name = target["name"]
order_of_targets_names.append(name)
# Logging
logging.info(f"Target sequence: {name}")
print("Target name:", name)
# Match the slices
for slice in slices:
name = slice["name"]
print("Slice name:", name)
slice_file = target["slices"][name]
print("Slice file:", slice_file)
sq = Sequence(slice_file)
json_to_output = {}
print("Sq name:", sq.name)
json_to_output["target"] = sq.name
json_to_output["slice"] = name # "revE"
# Get libs from template
libs = get_slices_libs(template)
print("Libs:", libs)
# Match slice
libs_to_match = libs[name]
matches = match_libs(sq, libs_to_match, threshold=threshold)
json_to_output["matches"] = matches
r.append(json_to_output)
# Write output result in JSON file
with open(match_output_filename, "w") as filename:
json.dump(r, filename, indent=2, separators=(",", ":"))
# Reconstruction
reconstruction_result = reconstruct(r)
print("Reconstruction:", reconstruction_result)
# Write reconstruction result in JSON file
with open(reconstruction_output_filename, "w") as filename:
json.dump(reconstruction_result, filename, indent=2, separators=(",", ":"))
# Extension and Addition to reconstruct the full pathway
ex = reconstruct_slices(reconstruction_result, template, targets)
print("Extension:", ex)
with open(extension_output_filename, "w") as filename:
json.dump(ex, filename, indent=2, separators=(",", ":"))
def run_test(test_params):
"""
Run tests
"""
targets = test_params["targets"]
template = test_params["template"]
nbloop = test_params["nbloop"]
test_id = test_params["id"]
test_name = test_params["name"]
threshold = test_params["threshold"]
OUTPUT_DIR = "output_results/"
# Logging configuration
timestr = time.strftime("%Y%m%d-%H%M%S")
logging.basicConfig(
format="%(asctime)s:%(levelname)s: %(message)s",
filename=f"logs/{current_file}-{test_id}-{timestr}.log",
encoding="utf-8",
level=logging.DEBUG,
)
msg = f"{test_name} - Targets:{path.basename(targets['file'])} - Template:{path.basename(template)} - Nb runs: {nbloop}"
logging.info(msg)
# Iterate and match libs over the input sequences above
for i in range(nbloop):
msg = f"Test run: ({i+1}/{nbloop})"
logging.info(msg)
# Match results filename
match_output_filename = f"{timestr}-matching-results-{current_file}-{test_id}-run-{i+1}-from-{nbloop}.json"
match_output_filename = path.join(OUTPUT_DIR, match_output_filename)
# Reconstruction results filename
reconstruction_output_filename = f"{timestr}-reconstruction-{current_file}-{test_id}-run-{i+1}-from-{nbloop}.json"
reconstruction_output_filename = path.join(
OUTPUT_DIR, reconstruction_output_filename
)
# Final results filename
extension_output_filename = (
f"{timestr}-extension-{current_file}-{test_id}-run-{i+1}-from-{nbloop}.json"
)
extension_output_filename = path.join(OUTPUT_DIR, extension_output_filename)
# Iterate and match libs
iter_all_seq(
targets,
template,
match_output_filename,
reconstruction_output_filename,
extension_output_filename,
threshold,
)
def main():
"""
Main
"""
pass
if __name__ == "__main__":
main()