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Add JSON output file with contamination results option #7

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35 changes: 30 additions & 5 deletions AuthentiCT/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@
import numdifftools as ndt
import pandas as pd
import random
import os
import json
from scipy.optimize import minimize


Expand Down Expand Up @@ -88,6 +90,10 @@ def get_configuration():
parser_inference.add_argument('--decoding', action='store_true',
help="Print the posterior probabilities of each state, one line per position\n"
"(default: False)")

parser_inference.add_argument('-j', '--json', action='store_true',
help="Output contamination results as JSON\n"
"(default: False)")


parser_deamination = subparsers.add_parser('deamination',
Expand Down Expand Up @@ -153,6 +159,9 @@ def get_configuration():

def main():

with open("test.txt", "w") as test_file:
test_file.write("Ici0")

options = get_configuration()

if options.command == "simulation":
Expand Down Expand Up @@ -194,10 +203,27 @@ def main():
print(list(fragments.keys())[list(fragments.values()).index(0)])
print("nodeam:", fragments["nodeam"], "; deam5:", fragments["deam5"], "; deam3:", fragments["deam3"], "; deam53:", fragments["deam53"], sep='\t')
return
total = fragments["nodeam"] + fragments["deam5"] + fragments["deam3"] + fragments["deam53"]
contamination = fragments["nodeam"] / total - fragments["deam5"] * fragments["deam3"] / (fragments["deam53"] * total)
print("#contamination_rate\t#nodeam\t#deam5\t#deam3\t#deam53", file=options.outputfile)
print(contamination, fragments["nodeam"], fragments["deam5"], fragments["deam3"], fragments["deam53"], sep='\t', file=options.outputfile)
else:
total = fragments["nodeam"] + fragments["deam5"] + fragments["deam3"] + fragments["deam53"]
contamination = fragments["nodeam"] / total - fragments["deam5"] * fragments["deam3"] / (fragments["deam53"] * total)

if options.json: # Check if the --json option is set
contamination_results = {
"contamination_rate": contamination,
"nodeam": fragments["nodeam"],
"deam5": fragments["deam5"],
"deam3": fragments["deam3"],
"deam53": fragments["deam53"]
}

# Save contamination results as JSON
output_filename = os.path.splitext(options.outputfile.name)[0] # Get the base filename without the extension
json_filename = f"{output_filename}_contamination_results.json"
with open(json_filename, "w") as json_file:
json.dump(contamination_results, json_file)

print("#contamination_rate\t#nodeam\t#deam5\t#deam3\t#deam53", file=options.outputfile)
print(contamination, fragments["nodeam"], fragments["deam5"], fragments["deam3"], fragments["deam53"], sep='\t', file=options.outputfile)
else:
if options.config:
param = np.array(read_parameters(options.config[0]))
Expand Down Expand Up @@ -245,4 +271,3 @@ def main():
print("Unrecognized command line argument")
if __name__ == '__main__':
main()