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| ##fileformat=VCFv4.2 | ||
| ##fileDate=20231001 | ||
| ##reference=GRCh38 | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO | ||
| 6 215879068 . C T . . . |
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Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,158 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "e5a89356", | ||
| "metadata": { | ||
| "tags": [ | ||
| "papermill-error-cell-tag" | ||
| ] | ||
| }, | ||
| "source": [ | ||
| "<span style=\"color:red; font-family:Helvetica Neue, Helvetica, Arial, sans-serif; font-size:2em;\">An Exception was encountered at '<a href=\"#papermill-error-cell\">In [1]</a>'.</span>" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "7fa11030", | ||
| "metadata": { | ||
| "tags": [ | ||
| "papermill-error-cell-tag" | ||
| ] | ||
| }, | ||
| "source": [ | ||
| "<span id=\"papermill-error-cell\" style=\"color:red; font-family:Helvetica Neue, Helvetica, Arial, sans-serif; font-size:2em;\">Execution using papermill encountered an exception here and stopped:</span>" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "id": "initial_id", | ||
| "metadata": { | ||
| "collapsed": true, | ||
| "execution": { | ||
| "iopub.execute_input": "2024-09-29T18:08:52.223851Z", | ||
| "iopub.status.busy": "2024-09-29T18:08:52.223339Z", | ||
| "iopub.status.idle": "2024-09-29T18:09:06.722487Z", | ||
| "shell.execute_reply": "2024-09-29T18:09:06.721642Z" | ||
| }, | ||
| "papermill": { | ||
| "duration": 14.503277, | ||
| "end_time": "2024-09-29T18:09:06.723475", | ||
| "exception": true, | ||
| "start_time": "2024-09-29T18:08:52.220198", | ||
| "status": "failed" | ||
| }, | ||
| "tags": [] | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "The file at ../data/lovd/lovd_data.txt already exists.\n" | ||
| ] | ||
| }, | ||
| { | ||
| "ename": "NoSuchWindowException", | ||
| "evalue": "Message: Browsing context has been discarded\nStacktrace:\nRemoteError@chrome://remote/content/shared/RemoteError.sys.mjs:8:8\nWebDriverError@chrome://remote/content/shared/webdriver/Errors.sys.mjs:193:5\nNoSuchWindowError@chrome://remote/content/shared/webdriver/Errors.sys.mjs:679:5\nassert.that/<@chrome://remote/content/shared/webdriver/Assert.sys.mjs:515:13\nassert.open@chrome://remote/content/shared/webdriver/Assert.sys.mjs:147:4\nGeckoDriver.prototype.navigateTo@chrome://remote/content/marionette/driver.sys.mjs:859:39\ndespatch@chrome://remote/content/marionette/server.sys.mjs:318:40\nexecute@chrome://remote/content/marionette/server.sys.mjs:289:16\nonPacket/<@chrome://remote/content/marionette/server.sys.mjs:262:20\nonPacket@chrome://remote/content/marionette/server.sys.mjs:263:9\n_onJSONObjectReady/<@chrome://remote/content/marionette/transport.sys.mjs:494:20\n", | ||
| "output_type": "error", | ||
| "traceback": [ | ||
| "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", | ||
| "\u001b[0;31mNoSuchWindowException\u001b[0m Traceback (most recent call last)", | ||
| "Cell \u001b[0;32mIn[1], line 13\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[38;5;66;03m# Fetch and process data\u001b[39;00m\n\u001b[1;32m 12\u001b[0m store_database_for_eys_gene(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlovd\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m)\n\u001b[0;32m---> 13\u001b[0m \u001b[43mstore_database_for_eys_gene\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mgnomad\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 15\u001b[0m lovd_data \u001b[38;5;241m=\u001b[39m parse_lovd(LOVD_PATH \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/lovd_data.txt\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 16\u001b[0m gnomad_data \u001b[38;5;241m=\u001b[39m parse_gnomad(GNOMAD_PATH \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m/gnomad_data.csv\u001b[39m\u001b[38;5;124m'\u001b[39m)\n", | ||
| "File \u001b[0;32m/mnt/c/Users/Vlad/PycharmProjects/kath/api/data/downloading.py:191\u001b[0m, in \u001b[0;36mstore_database_for_eys_gene\u001b[0;34m(database_name, override)\u001b[0m\n\u001b[1;32m 189\u001b[0m download_lovd_database_for_eys_gene(override)\n\u001b[1;32m 190\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 191\u001b[0m \u001b[43mdownload_database_for_eys_gene\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdatabase_name\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43moverride\u001b[49m\u001b[43m)\u001b[49m\n", | ||
| "File \u001b[0;32m/mnt/c/Users/Vlad/PycharmProjects/kath/api/data/downloading.py:167\u001b[0m, in \u001b[0;36mdownload_database_for_eys_gene\u001b[0;34m(database_name, override)\u001b[0m\n\u001b[1;32m 163\u001b[0m firefox_options\u001b[38;5;241m.\u001b[39mset_preference(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mbrowser.helperApps.neverAsk.saveToDisk\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 164\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mapplication/octet-stream\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 166\u001b[0m driver \u001b[38;5;241m=\u001b[39m webdriver\u001b[38;5;241m.\u001b[39mFirefox(options\u001b[38;5;241m=\u001b[39mfirefox_options)\n\u001b[0;32m--> 167\u001b[0m \u001b[43mdriver\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43murl\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 168\u001b[0m WebDriverWait(driver, \u001b[38;5;241m30\u001b[39m)\u001b[38;5;241m.\u001b[39muntil(EC\u001b[38;5;241m.\u001b[39melement_to_be_clickable((By\u001b[38;5;241m.\u001b[39mXPATH, clickable)))\n\u001b[1;32m 169\u001b[0m driver\u001b[38;5;241m.\u001b[39mexecute_script(button_location)\n", | ||
| "File \u001b[0;32m~/.local/lib/python3.10/site-packages/selenium/webdriver/remote/webdriver.py:363\u001b[0m, in \u001b[0;36mWebDriver.get\u001b[0;34m(self, url)\u001b[0m\n\u001b[1;32m 361\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget\u001b[39m(\u001b[38;5;28mself\u001b[39m, url: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 362\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Loads a web page in the current browser session.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 363\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43mCommand\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mGET\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m{\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43murl\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m}\u001b[49m\u001b[43m)\u001b[49m\n", | ||
| "File \u001b[0;32m~/.local/lib/python3.10/site-packages/selenium/webdriver/remote/webdriver.py:354\u001b[0m, in \u001b[0;36mWebDriver.execute\u001b[0;34m(self, driver_command, params)\u001b[0m\n\u001b[1;32m 352\u001b[0m response \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcommand_executor\u001b[38;5;241m.\u001b[39mexecute(driver_command, params)\n\u001b[1;32m 353\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m response:\n\u001b[0;32m--> 354\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43merror_handler\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mresponse\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 355\u001b[0m response[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mvalue\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_unwrap_value(response\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mvalue\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m))\n\u001b[1;32m 356\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m response\n", | ||
| "File \u001b[0;32m~/.local/lib/python3.10/site-packages/selenium/webdriver/remote/errorhandler.py:229\u001b[0m, in \u001b[0;36mErrorHandler.check_response\u001b[0;34m(self, response)\u001b[0m\n\u001b[1;32m 227\u001b[0m alert_text \u001b[38;5;241m=\u001b[39m value[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124malert\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtext\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 228\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m exception_class(message, screen, stacktrace, alert_text) \u001b[38;5;66;03m# type: ignore[call-arg] # mypy is not smart enough here\u001b[39;00m\n\u001b[0;32m--> 229\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m exception_class(message, screen, stacktrace)\n", | ||
| "\u001b[0;31mNoSuchWindowException\u001b[0m: Message: Browsing context has been discarded\nStacktrace:\nRemoteError@chrome://remote/content/shared/RemoteError.sys.mjs:8:8\nWebDriverError@chrome://remote/content/shared/webdriver/Errors.sys.mjs:193:5\nNoSuchWindowError@chrome://remote/content/shared/webdriver/Errors.sys.mjs:679:5\nassert.that/<@chrome://remote/content/shared/webdriver/Assert.sys.mjs:515:13\nassert.open@chrome://remote/content/shared/webdriver/Assert.sys.mjs:147:4\nGeckoDriver.prototype.navigateTo@chrome://remote/content/marionette/driver.sys.mjs:859:39\ndespatch@chrome://remote/content/marionette/server.sys.mjs:318:40\nexecute@chrome://remote/content/marionette/server.sys.mjs:289:16\nonPacket/<@chrome://remote/content/marionette/server.sys.mjs:262:20\nonPacket@chrome://remote/content/marionette/server.sys.mjs:263:9\n_onJSONObjectReady/<@chrome://remote/content/marionette/transport.sys.mjs:494:20\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "import os\n", | ||
| "from api.data.refactoring import merge_gnomad_lovd, parse_gnomad, set_gnomad_dtypes\n", | ||
| "from api import (store_database_for_eys_gene,\n", | ||
| " parse_lovd,\n", | ||
| " set_lovd_dtypes,\n", | ||
| " LOVD_PATH,\n", | ||
| " GNOMAD_PATH)\n", | ||
| "import pandas as pd\n", | ||
| "from tests.tools.spliceai.spliceai import add_spliceai_eval_column\n", | ||
| "\n", | ||
| "# Fetch and process data\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 correct data types for LOVD and gnomAD data\n", | ||
| "set_lovd_dtypes(lovd_data)\n", | ||
| "set_gnomad_dtypes(gnomad_data)\n", | ||
| "\n", | ||
| "# Prepare LOVD data for merging\n", | ||
| "variants_on_genome = lovd_data[\"Variants_On_Genome\"].copy()\n", | ||
| "lovd_data = pd.merge(lovd_data[\"Variants_On_Transcripts\"],\n", | ||
| " variants_on_genome[['id', 'VariantOnGenome/DNA', 'VariantOnGenome/DNA/hg38',\n", | ||
| " 'chromosome', 'position_g_start', 'position_g_end']],\n", | ||
| " on='id',\n", | ||
| " how='left')\n", | ||
| "\n", | ||
| "gnomad_data = gnomad_data.copy()\n", | ||
| "data = merge_gnomad_lovd(lovd_data, gnomad_data)\n", | ||
| "first_100_rows = data.head(100).copy()\n", | ||
| "\n", | ||
| "# Define path for FASTA file\n", | ||
| "fasta_path = \"hg38_chr6.fa\"\n", | ||
| "\n", | ||
| "print(f\"Current working directory: {os.getcwd()}\")\n", | ||
| "# Verify the FASTA file's existence\n", | ||
| "if os.path.isfile(fasta_path):\n", | ||
| " print(\"FASTA file exists and can be read.\")\n", | ||
| "else:\n", | ||
| " print(f\"FASTA file not found at path: {fasta_path}\")\n", | ||
| " raise FileNotFoundError(f\"FASTA file not found at path: {fasta_path}\")\n", | ||
| "\n", | ||
| "result_data_spliceai = add_spliceai_eval_column(first_100_rows, fasta_path)\n", | ||
| "\n", | ||
| "# Output the result with SpliceAI scores\n", | ||
| "result_data_spliceai" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.10.12" | ||
| }, | ||
| "papermill": { | ||
| "default_parameters": {}, | ||
| "duration": 22.483974, | ||
| "end_time": "2024-09-29T18:09:09.346454", | ||
| "environment_variables": {}, | ||
| "exception": true, | ||
| "input_path": "tests/spliceai_test.ipynb", | ||
| "output_path": "tests/output.ipynb", | ||
| "parameters": {}, | ||
| "start_time": "2024-09-29T18:08:46.862480", | ||
| "version": "2.6.0" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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