From c5d370cb4731d895ff1a9683d7d245c9c096fda8 Mon Sep 17 00:00:00 2001 From: Tarun Mamidi Date: Fri, 26 Jan 2024 14:37:30 -0600 Subject: [PATCH] ignores python notebook links for linting --- docs/build_DITTO.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/build_DITTO.md b/docs/build_DITTO.md index 47b16ff..5a490df 100644 --- a/docs/build_DITTO.md +++ b/docs/build_DITTO.md @@ -86,9 +86,11 @@ python src/annotation_parsing/parse_single_sample.py -i clinvar.vcf.gz.variant.c -o clinvar.vcf.gz.variant.csv_parsed.csv.gz -c configs/opencravat_train_config.json ``` + Filter and process the annotations as shown in this [python -notebook](src/annotation_parsing/opencravat_clinvar_filtering_80-20-20.ipynb). This will output training and testing +notebook](../src/annotation_parsing/opencravat_clinvar_filtering_80-20-20.ipynb). This will output training and testing data to train the neural network. + ## Tune and Train DITTO @@ -117,6 +119,7 @@ Follow the below steps to install and add more databases for annotation and befo 4. Follow the steps from Preprocessing above to parse, filter, process, tune and train DITTO. ## Benchmarking - -Please follow the [python notebook](../../src/analysis/opencravat_latest_benchmarking-Consequence_80_20.ipynb) to benchmark + +Please follow the [python notebook](../src/analysis/opencravat_latest_benchmarking-Consequence_80_20.ipynb) to benchmark DITTO with other pathogenicity predition tools. It also has code snippets to generate testing metrics and SHAP plots. +