diff --git a/tests/pipeline.ipynb b/tests/pipeline.ipynb index 71cf21d..1382b31 100644 --- a/tests/pipeline.ipynb +++ b/tests/pipeline.ipynb @@ -238,10 +238,38 @@ { "metadata": {}, "cell_type": "code", - "source": "", - "id": "6f0abfb50bd211a0", "outputs": [], - "execution_count": null + "execution_count": null, + "source": [ + "from api.data.refactoring import merge_gnomad_lovd, parse_gnomad, set_gnomad_dtypes\n", + "import pandas as pd\n", + "from api import (store_database_for_eys_gene,\n", + " parse_lovd,\n", + " set_lovd_dtypes,\n", + " LOVD_PATH,\n", + " GNOMAD_PATH)\n", + "\n", + "store_database_for_eys_gene('lovd', False)\n", + "store_database_for_eys_gene('gnomad', False)\n", + "\n", + "lovd_data = parse_lovd(LOVD_PATH + \"/lovd_data.txt\")\n", + "gnomad_data = parse_gnomad(GNOMAD_PATH+'/gnomad_data.csv')\n", + "\n", + "set_lovd_dtypes(lovd_data)\n", + "set_gnomad_dtypes(gnomad_data)\n", + "\n", + "variants_on_genome = lovd_data[\"Variants_On_Genome\"].copy()\n", + "\n", + "lovd_data = pd.merge(lovd_data[\"Variants_On_Transcripts\"],\n", + " variants_on_genome[['id','VariantOnGenome/DNA','VariantOnGenome/DNA/hg38']],\n", + " on='id',\n", + " how='left')\n", + "\n", + "gnomad_data = gnomad_data.copy()\n", + "final_data = merge_gnomad_lovd(lovd_data, gnomad_data)\n", + "final_data" + ], + "id": "ba435cd29d565f7d" } ], "metadata": {