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pnrobinson committed Dec 24, 2024
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158 changes: 158 additions & 0 deletions notebooks/SPATA22/SPATA22_SPGF96_individuals.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# SPATA22\n",
"[spermatogenic failure-96 (SPGF96)](https://omim.org/entry/621001) is caused by homozygous mutation in the SPATA22 gene."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Using pyphetools version 0.9.115\n"
]
}
],
"source": [
"from pyphetools.creation import TemplateImporter, Moi\n",
"from pyphetools.visualization import IndividualTable, QcVisualizer\n",
"from IPython.display import display, HTML\n",
"import pyphetools\n",
"print(f\"Using pyphetools version {pyphetools.__version__}\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"HPO version 2024-12-12\n",
"Created encoders for 23 fields\n",
"Importing OMIM:621001, Spermatogenic failure 96, HGNC:30705, SPATA22, NM_001170698.2\n",
"[INFO] encoding variant \"c.400C>T\"\n",
"https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001170698.2%3Ac.400C>T/NM_001170698.2?content-type=application%2Fjson\n",
"[INFO] encoding variant \"c.203del\"\n",
"https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001170698.2%3Ac.203del/NM_001170698.2?content-type=application%2Fjson\n",
"We output 3 GA4GH phenopackets to the directory phenopackets\n"
]
}
],
"source": [
"template = \"input/SPATA22_SPGF96_individuals.xlsx\"\n",
"created_by = \"0000-0002-0736-9199\"\n",
"timporter = TemplateImporter(template=template, created_by=created_by)\n",
"individual_list, cvalidator = timporter.import_phenopackets_from_template()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<h2>Cohort validation</h2>\n",
"<p>No errors found for the cohort with 3 individuals</p>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"qc = QcVisualizer(cohort_validator=cvalidator)\n",
"display(HTML(qc.to_summary_html()))"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table style=\"border: 2px solid black; align: \"left\">\n",
"<caption>3 phenopackets - PMID:34392356 (n=1); PMID:35285020 (n=2)</caption>\n",
"<tr><th style=\"text-align: left;font-weight: bold;\">Individual</th><th style=\"text-align: left;font-weight: bold;\">Disease</th><th style=\"text-align: left;font-weight: bold;\">Genotype</th><th style=\"text-align: left;font-weight: bold;\">Phenotypic features</th></tr>\n",
"<tr><td style=\"text-align: left;\">nan (MALE)</td><td style=\"text-align: left;\">Spermatogenic failure 96 (OMIM:621001)</td><td style=\"text-align: left;\">NM_001170698.2:c.203del (homozygous)</td><td style=\"text-align: left;\">Non-obstructive azoospermia (HP:0011961): onset ; Male infertility (HP:0003251): onset </td></tr>\n",
"<tr><td style=\"text-align: left;\">proband IV-3 (MALE; P23Y)</td><td style=\"text-align: left;\">Spermatogenic failure 96 (OMIM:621001)</td><td style=\"text-align: left;\">NM_001170698.2:c.400C>T (homozygous)</td><td style=\"text-align: left;\">Non-obstructive azoospermia (HP:0011961): onset ; Spermatocyte maturation arrest (HP:0031039): onset ; Male infertility (HP:0003251): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Abnormal circulating testosterone concentration (HP:0030087): onset ; excluded: Abnormal circulating gonadotropin concentration (HP:0030338): onset </td></tr>\n",
"<tr><td style=\"text-align: left;\">brother IV-4 (MALE; P21Y)</td><td style=\"text-align: left;\">Spermatogenic failure 96 (OMIM:621001)</td><td style=\"text-align: left;\">NM_001170698.2:c.400C>T (homozygous)</td><td style=\"text-align: left;\">Non-obstructive azoospermia (HP:0011961): onset ; Male infertility (HP:0003251): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Abnormal circulating testosterone concentration (HP:0030087): onset ; excluded: Abnormal circulating gonadotropin concentration (HP:0030338): onset </td></tr>\n",
"</table>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"table = IndividualTable(cvalidator.get_error_free_individual_list())\n",
"display(HTML(table.to_html()))"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[pyphetools] Ingested 3 GA4GH phenopackets.\n",
"[INFO] Extracted 3 from 3 phenopackets with OMIM:621001\n",
"\n",
"\tSpermatogenic failure 96 (OMIM:621001): n=3\n",
"We found a total of 6 unique HPO terms\n",
"Extracted disease: Spermatogenic failure 96 (OMIM:621001)\n",
"Wrote HPOA disease file to OMIM-621001.tab\n"
]
}
],
"source": [
"pmid = \"PMID:34392356\"\n",
"df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:621001\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "ps24venv",
"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": "3.12.4"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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141 changes: 141 additions & 0 deletions notebooks/SPATA22/phenopackets/PMID_34392356_nan.json
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{
"id": "PMID_34392356_nan",
"subject": {
"id": "nan",
"vitalStatus": {
"status": "ALIVE"
},
"sex": "MALE"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0011961",
"label": "Non-obstructive azoospermia"
}
},
{
"type": {
"id": "HP:0003251",
"label": "Male infertility"
}
}
],
"interpretations": [
{
"id": "nan",
"progressStatus": "SOLVED",
"diagnosis": {
"disease": {
"id": "OMIM:621001",
"label": "Spermatogenic failure 96"
},
"genomicInterpretations": [
{
"subjectOrBiosampleId": "nan",
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"variationDescriptor": {
"id": "var_NzjHkpwFoSKRneSdxLMvyCPHy",
"geneContext": {
"valueId": "HGNC:30705",
"symbol": "SPATA22"
},
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_001170698.2:c.203del"
},
{
"syntax": "hgvs.g",
"value": "NC_000017.11:g.3462738del"
}
],
"vcfRecord": {
"genomeAssembly": "hg38",
"chrom": "chr17",
"pos": "3462736",
"ref": "CA",
"alt": "C"
},
"moleculeContext": "genomic",
"allelicState": {
"id": "GENO:0000136",
"label": "homozygous"
}
}
}
}
]
}
}
],
"diseases": [
{
"term": {
"id": "OMIM:621001",
"label": "Spermatogenic failure 96"
},
"onset": {
"ontologyClass": {
"id": "HP:0011462",
"label": "Young adult onset"
}
}
}
],
"metaData": {
"created": "2024-12-24T08:56:45.910399913Z",
"createdBy": "ORCID:0000-0002-0736-9199",
"resources": [
{
"id": "geno",
"name": "Genotype Ontology",
"url": "http://purl.obolibrary.org/obo/geno.owl",
"version": "2022-03-05",
"namespacePrefix": "GENO",
"iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
},
{
"id": "hgnc",
"name": "HUGO Gene Nomenclature Committee",
"url": "https://www.genenames.org",
"version": "06/01/23",
"namespacePrefix": "HGNC",
"iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
},
{
"id": "omim",
"name": "An Online Catalog of Human Genes and Genetic Disorders",
"url": "https://www.omim.org",
"version": "January 4, 2023",
"namespacePrefix": "OMIM",
"iriPrefix": "https://www.omim.org/entry/"
},
{
"id": "so",
"name": "Sequence types and features ontology",
"url": "http://purl.obolibrary.org/obo/so.obo",
"version": "2021-11-22",
"namespacePrefix": "SO",
"iriPrefix": "http://purl.obolibrary.org/obo/SO_"
},
{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2024-12-12",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
],
"phenopacketSchemaVersion": "2.0",
"externalReferences": [
{
"id": "PMID:34392356",
"reference": "https://pubmed.ncbi.nlm.nih.gov/34392356",
"description": "Whole-exome sequencing of consanguineous families with infertile men and women identifies homologous mutations in SPATA22 and MEIOB"
}
]
}
}
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