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AMT
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pnrobinson committed Jan 10, 2025
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160 changes: 160 additions & 0 deletions notebooks/AMT/AMT_GCE2_individuals.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# AMT\n",
"[glycine encephalopathy-2 (GCE2)](https://omim.org/entry/620398) is caused by homozygous or compound heterozygous mutation in the AMT gene."
]
},
{
"cell_type": "code",
"execution_count": 8,
"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": 13,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"HPO version 2024-12-12\n",
"Created encoders for 38 fields\n",
"Importing OMIM:620398, Glycine encephalopathy 2, HGNC:473, AMT, NM_000481.4\n",
"We output 5 GA4GH phenopackets to the directory phenopackets\n"
]
}
],
"source": [
"template = \"input/AMT_GCE2_individuals.xlsx\"\n",
"created_by = \"0000-0002-0736-9199\"\n",
"deletions = {\"DEL:Total AMT gene deletion\"}\n",
"timporter = TemplateImporter(template=template, created_by=created_by)\n",
"individual_list, cvalidator = timporter.import_phenopackets_from_template(deletions=deletions)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<h2>Cohort validation</h2>\n",
"<p>No errors found for the cohort with 5 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": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table style=\"border: 2px solid black; align: \"left\">\n",
"<caption>5 phenopackets - PMID:8005589 (n=2); PMID:9600239 (n=1); PMID:33791923 (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;\">patient A (FEMALE; P19Y)</td><td style=\"text-align: left;\">Glycine encephalopathy 2 (OMIM:620398)</td><td style=\"text-align: left;\">NM_000481.4:c.806G>A (homozygous)</td><td style=\"text-align: left;\">Global developmental delay (HP:0001263): onset ; Hyperglycinuria (HP:0003108): onset ; Intellectual disability, severe (HP:0010864): onset </td></tr>\n",
"<tr><td style=\"text-align: left;\">patient B (FEMALE; P9Y)</td><td style=\"text-align: left;\">Glycine encephalopathy 2 (OMIM:620398)</td><td style=\"text-align: left;\"><ul> <li>NM_000481.4:c.139G>A (heterozygous)</li> <li>NM_000481.4:c.959G>A (heterozygous)</li> </ul></td><td style=\"text-align: left;\">Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; Cerebral atrophy (HP:0002059): onset ; Hyperglycinuria (HP:0003108): onset ; Intellectual disability, severe (HP:0010864): onset </td></tr>\n",
"<tr><td style=\"text-align: left;\"> propositus VII-7 (MALE; P2D)</td><td style=\"text-align: left;\">Glycine encephalopathy 2 (OMIM:620398)</td><td style=\"text-align: left;\">NM_000481.4:c.125A>G (homozygous)</td><td style=\"text-align: left;\">EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset <br/><b>TimeElement(element=Age(iso8601duration=P2D))</b>: Seizure (HP:0001250): onset age {\n",
" iso8601duration: \"P2D\"\n",
"}\n",
"</td></tr>\n",
"<tr><td style=\"text-align: left;\">Patient 6 (FEMALE; P5D)</td><td style=\"text-align: left;\">Glycine encephalopathy 2 (OMIM:620398)</td><td style=\"text-align: left;\">NM_000481.4:c.434A>T (homozygous)</td><td style=\"text-align: left;\">Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset ; Respiratory failure requiring assisted ventilation (HP:0004887): onset ; Patent foramen ovale (HP:0001655): onset ; Microcephaly (HP:0000252): onset ; Hypotonia (HP:0001252): onset ; Vomiting (HP:0002013): onset ; Pyloric stenosis (HP:0002021): onset ; Micrognathia (HP:0000347): onset ; Hyperreflexia (HP:0001347): onset ; Poor suck (HP:0002033): onset ; Dysplastic corpus callosum (HP:0006989): onset ; Cerebral hypomyelination (HP:0006808): onset ; excluded: Hydrocephalus (HP:0000238): onset ; excluded: Ventriculomegaly (HP:0002119): onset </td></tr>\n",
"<tr><td style=\"text-align: left;\">Patient 7 (MALE; P7Y5M)</td><td style=\"text-align: left;\">Glycine encephalopathy 2 (OMIM:620398)</td><td style=\"text-align: left;\">DEL:Total AMT gene deletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset ; Respiratory failure requiring assisted ventilation (HP:0004887): onset ; Microcephaly (HP:0000252): onset ; Hypotonia (HP:0001252): onset ; Micrognathia (HP:0000347): onset ; Hyperreflexia (HP:0001347): onset ; Poor suck (HP:0002033): onset ; Dysplastic corpus callosum (HP:0006989): onset ; Hydrocephalus (HP:0000238): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Vomiting (HP:0002013): onset ; excluded: Pyloric stenosis (HP:0002021): onset ; excluded: Cerebral hypomyelination (HP:0006808): onset ; excluded: Ventriculomegaly (HP:0002119): 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": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[pyphetools] Ingested 5 GA4GH phenopackets.\n",
"[INFO] Extracted 5 from 5 phenopackets with OMIM:620398\n",
"\n",
"\tGlycine encephalopathy 2 (OMIM:620398): n=5\n",
"We found a total of 21 unique HPO terms\n",
"Extracted disease: Glycine encephalopathy 2 (OMIM:620398)\n",
"Wrote HPOA disease file to OMIM-620398.tab\n"
]
}
],
"source": [
"pmid = \"PMID:8005589\"\n",
"df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:620398\")"
]
}
],
"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": "3.12.8"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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