diff --git a/notebooks/STXBP1/STXBP1.ipynb b/notebooks/STXBP1/STXBP1.ipynb new file mode 100644 index 00000000..59c27b18 --- /dev/null +++ b/notebooks/STXBP1/STXBP1.ipynb @@ -0,0 +1,166 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "9dc963e1", + "metadata": {}, + "source": [ + "

STXBP1 genotype-phenotype correlation analysis

\n", + "

todo

" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "492f5c98", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using genophenocorr version 0.1.1dev\n" + ] + } + ], + "source": [ + "import genophenocorr\n", + "print(f\"Using genophenocorr version {genophenocorr.__version__}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "c0692465", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loaded HPO v2022-10-05\n" + ] + } + ], + "source": [ + "import hpotk\n", + "hpo_purl = \"/Users/robinp/data/hpo/hp.json\"\n", + "hpo = hpotk.load_minimal_ontology(hpo_purl)\n", + "print(f'Loaded HPO v{hpo.version}')" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "77660956-d30f-4c49-a4a0-7fdae1e75b9f", + "metadata": {}, + "outputs": [], + "source": [ + "from genophenocorr.preprocessing import configure_caching_patient_creator\n", + "patient_creator = configure_caching_patient_creator(hpo)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "76967087-8fde-4388-95d2-dba1776bfa08", + "metadata": {}, + "outputs": [], + "source": [ + "from genophenocorr.preprocessing import load_phenopacket_folder" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "3c07a0a5-560a-4970-9f6e-deed8f06fe35", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Expected a result but got an Error for variant: 9_127684372_127684373_A_A_heterozygous\n" + ] + }, + { + "ename": "HTTPError", + "evalue": "400 Client Error: Bad Request for url: https://rest.ensembl.org/vep/human/region/9:127684373-127684373/A?LoF=1&canonical=1&domains=1&hgvs=1&mutfunc=1&numbers=1&protein=1&refseq=1&mane=1&transcript_version=1&variant_class=1", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mHTTPError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[5], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m phenopacket_input_folder \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minput\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m----> 2\u001b[0m patient_list \u001b[38;5;241m=\u001b[39m \u001b[43mload_phenopacket_folder\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpp_directory\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mphenopacket_input_folder\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpatient_creator\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpatient_creator\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_phenopacket.py:196\u001b[0m, in \u001b[0;36mload_phenopacket_folder\u001b[0;34m(pp_directory, patient_creator)\u001b[0m\n\u001b[1;32m 193\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo JSON Phenopackets were found in \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpp_directory\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 195\u001b[0m \u001b[38;5;66;03m# turn phenopackets into patients using patient creator\u001b[39;00m\n\u001b[0;32m--> 196\u001b[0m patients \u001b[38;5;241m=\u001b[39m [patient_creator\u001b[38;5;241m.\u001b[39mcreate_patient(pp) \u001b[38;5;28;01mfor\u001b[39;00m pp \u001b[38;5;129;01min\u001b[39;00m pps]\n\u001b[1;32m 198\u001b[0m \u001b[38;5;66;03m# create cohort from patients\u001b[39;00m\n\u001b[1;32m 199\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m Cohort\u001b[38;5;241m.\u001b[39mfrom_patients(patients)\n", + "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_phenopacket.py:196\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 193\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo JSON Phenopackets were found in \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpp_directory\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 195\u001b[0m \u001b[38;5;66;03m# turn phenopackets into patients using patient creator\u001b[39;00m\n\u001b[0;32m--> 196\u001b[0m patients \u001b[38;5;241m=\u001b[39m [\u001b[43mpatient_creator\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_patient\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpp\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m pp \u001b[38;5;129;01min\u001b[39;00m pps]\n\u001b[1;32m 198\u001b[0m \u001b[38;5;66;03m# create cohort from patients\u001b[39;00m\n\u001b[1;32m 199\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m Cohort\u001b[38;5;241m.\u001b[39mfrom_patients(patients)\n", + "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_phenopacket.py:116\u001b[0m, in \u001b[0;36mPhenopacketPatientCreator.create_patient\u001b[0;34m(self, item)\u001b[0m\n\u001b[1;32m 108\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Creates a Patient from the data in a given Phenopacket\u001b[39;00m\n\u001b[1;32m 109\u001b[0m \n\u001b[1;32m 110\u001b[0m \u001b[38;5;124;03mArgs:\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 113\u001b[0m \u001b[38;5;124;03m Patient: A Patient object\u001b[39;00m\n\u001b[1;32m 114\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 115\u001b[0m phenotypes \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_phenotypes(item)\n\u001b[0;32m--> 116\u001b[0m variants \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_add_variants\u001b[49m\u001b[43m(\u001b[49m\u001b[43mitem\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 117\u001b[0m protein_data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_protein_data(variants)\n\u001b[1;32m 118\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m Patient(item\u001b[38;5;241m.\u001b[39mid, phenotypes, variants, protein_data)\n", + "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_phenopacket.py:136\u001b[0m, in \u001b[0;36mPhenopacketPatientCreator._add_variants\u001b[0;34m(self, pp)\u001b[0m\n\u001b[1;32m 134\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_logger\u001b[38;5;241m.\u001b[39mwarning(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPatient \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpp\u001b[38;5;241m.\u001b[39mid\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m has unknown alternative variant \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mvc\u001b[38;5;241m.\u001b[39malt\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m and will not be included.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 135\u001b[0m \u001b[38;5;28;01mcontinue\u001b[39;00m\n\u001b[0;32m--> 136\u001b[0m variant \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_func_ann\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mannotate\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvc\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 137\u001b[0m variants_list\u001b[38;5;241m.\u001b[39mappend(variant)\n\u001b[1;32m 138\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", + "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_variant.py:227\u001b[0m, in \u001b[0;36mVarCachingFunctionalAnnotator.annotate\u001b[0;34m(self, variant_coordinates)\u001b[0m\n\u001b[1;32m 225\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m annotations\n\u001b[1;32m 226\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 227\u001b[0m ann \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fallback\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mannotate\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvariant_coordinates\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 228\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache\u001b[38;5;241m.\u001b[39mstore_annotations(variant_coordinates, ann)\n\u001b[1;32m 229\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ann\n", + "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_variant.py:79\u001b[0m, in \u001b[0;36mVepFunctionalAnnotator.annotate\u001b[0;34m(self, variant_coordinates)\u001b[0m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mannotate\u001b[39m(\u001b[38;5;28mself\u001b[39m, variant_coordinates: VariantCoordinates) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Variant:\n\u001b[1;32m 72\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Creates a Variant object by searching variant coordinates with Variant Effect Predictor (VEP) REST API. \u001b[39;00m\n\u001b[1;32m 73\u001b[0m \n\u001b[1;32m 74\u001b[0m \u001b[38;5;124;03m Args:\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 77\u001b[0m \u001b[38;5;124;03m Variant: A Variant object\u001b[39;00m\n\u001b[1;32m 78\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m---> 79\u001b[0m variant \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_query_vep\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvariant_coordinates\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 80\u001b[0m variant_id \u001b[38;5;241m=\u001b[39m variant\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mid\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 81\u001b[0m variant_class \u001b[38;5;241m=\u001b[39m variant\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mvariant_class\u001b[39m\u001b[38;5;124m'\u001b[39m)\n", + "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_variant.py:130\u001b[0m, in \u001b[0;36mVepFunctionalAnnotator._query_vep\u001b[0;34m(self, variant_coordinates)\u001b[0m\n\u001b[1;32m 128\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m r\u001b[38;5;241m.\u001b[39mok:\n\u001b[1;32m 129\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_logging\u001b[38;5;241m.\u001b[39merror(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mExpected a result but got an Error for variant: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mvariant_coordinates\u001b[38;5;241m.\u001b[39mas_string()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 130\u001b[0m \u001b[43mr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mraise_for_status\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 131\u001b[0m results \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mjson()\n\u001b[1;32m 132\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(results, \u001b[38;5;28mlist\u001b[39m):\n", + "File \u001b[0;32m~/GIT/genophenocorr/gpc2venv/lib/python3.8/site-packages/requests/models.py:1021\u001b[0m, in \u001b[0;36mResponse.raise_for_status\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1016\u001b[0m http_error_msg \u001b[38;5;241m=\u001b[39m (\n\u001b[1;32m 1017\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstatus_code\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Server Error: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mreason\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m for url: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39murl\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1018\u001b[0m )\n\u001b[1;32m 1020\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m http_error_msg:\n\u001b[0;32m-> 1021\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m HTTPError(http_error_msg, response\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m)\n", + "\u001b[0;31mHTTPError\u001b[0m: 400 Client Error: Bad Request for url: https://rest.ensembl.org/vep/human/region/9:127684373-127684373/A?LoF=1&canonical=1&domains=1&hgvs=1&mutfunc=1&numbers=1&protein=1&refseq=1&mane=1&transcript_version=1&variant_class=1" + ] + } + ], + "source": [ + "phenopacket_input_folder = \"input\"\n", + "patient_list = load_phenopacket_folder(pp_directory=phenopacket_input_folder, patient_creator=patient_creator)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a41be80d-0678-4dc3-97b6-2876d69648e0", + "metadata": {}, + "outputs": [], + "source": [ + "from genophenocorr.model import Cohort\n", + "from genophenocorr.view import CohortViewer\n", + "from IPython.display import display, HTML\n", + "cohort = Cohort.from_patients(patient_list)" + ] + }, + { + "cell_type": "markdown", + "id": "175d2b14-b75a-499a-9251-5154aa31c683", + "metadata": {}, + "source": [ + "

CohortViewer

\n", + "

The CohortViewer class offers various methods to create tables and graphics to view the data in the cohort.\n", + "It is still very much in progress

" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1c7c5c1e-8e5e-488a-98ec-85689adff61c", + "metadata": {}, + "outputs": [], + "source": [ + "viewer = CohortViewer(hpo=hpo)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "gpc2venv", + "language": "python", + "name": "gpc2venv" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/STXBP1/input/PMID_35190816_STX_102.json b/notebooks/STXBP1/input/PMID_35190816_STX_102.json new file mode 100644 index 00000000..fcceb70a --- /dev/null +++ b/notebooks/STXBP1/input/PMID_35190816_STX_102.json @@ -0,0 +1,140 @@ +{ + "id": "STX_102", + "subject": { + "id": "STX_102", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P25Y" + } + } + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0002360", + "label": "Sleep disturbance" + } + }, + { + "type": { + "id": "HP:0007359", + "label": "Focal-onset seizure" + } + }, + { + "type": { + "id": "HP:0000717", + "label": "Autism" + } + }, + { + "type": { + "id": "HP:0002342", + "label": "Intellectual disability, moderate" + } + } + ], + "interpretations": [ + { + "id": "STX_102", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:602926c", + "label": "NDD" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "STX_102", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_QNjawtALouzsBvwKjYXyBdCvT", + "geneContext": { + "valueId": "HGNC:11444", + "symbol": "STXBP1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001032221.6:c.1501_1519del" + }, + { + "syntax": "hgvs.g", + "value": "NC_000009.12:g.127680196_127680214del" + } + ], + "vcfRecord": { + 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