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Data tables to JSON files#18

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lxhlxhlxh555 wants to merge 2 commits into
PGP-UK:mainfrom
lxhlxhlxh555:gVCF_entrypoint_py
Open

Data tables to JSON files#18
lxhlxhlxh555 wants to merge 2 commits into
PGP-UK:mainfrom
lxhlxhlxh555:gVCF_entrypoint_py

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@lxhlxhlxh555

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  1. Codes have been further split for modularity.
  2. Added code comments for clarity.
  3. Added the function to export data tables to JSON files for the front-end.

Relevant test files and commands are as follows:

Total pipeline test:

python3 main.py --vcf data/NA12878wxs.g.vcf --vep data/tester_1_VEP.html --resultsDir output/sample --GATKthreads 8
python3 main.py --bamFile data/NA12878wxs.bam --vep data/tester_1_VEP.html --resultsDir output/sample  --GATKthreads 8

or function test:

python3 scripts/to_front_jsons.py geno_tables_to_jsons data/sample/tables_full output/test/front_jsons
python3 scripts/to_front_jsons.py vep_labex_tables_to_jsons data/sample/vep_dir data/sample/latex output/test/front_jsons

tables_full.zip
vep_dir.zip
latex.zip
tester_1_VEP.html.zip

@IsmailM IsmailM changed the base branch from gVCF_entrypoint to master August 29, 2023 13:13
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