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Add JSON output file with contamination results option#7

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JuPrgn wants to merge 1 commit intoStephanePeyregne:masterfrom
JuPrgn:add_json_conta_result
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Add JSON output file with contamination results option#7
JuPrgn wants to merge 1 commit intoStephanePeyregne:masterfrom
JuPrgn:add_json_conta_result

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@JuPrgn
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@JuPrgn JuPrgn commented Oct 19, 2023

Relates to #4

Add json option -j to save contamination results in [output name]_contamination_results.json (only with terminal option active)

Command : python AuthentiCT deam2cont -t -j -o out.txt -s 10000 test_dataset\Sima.incisor.subset_test.sam

Generates following files :

out.txt

#contamination_rate	#nodeam	#deam5	#deam3	#deam53
0.8671328671328671	174	6	5	13

out_contamination_results.json

{"contamination_rate": 0.8671328671328671, "nodeam": 174, "deam5": 6, "deam3": 5, "deam53": 13}

@apeltzer
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Looks like a MultiQC module might be available soon ;-)

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