Create a Gene Shet reference data update cmd.

CHANGELOG.md

@@ -1,6 +1,7 @@
 # _seqr_ Changes
 
 ## dev
+* Add GeneShet model to the reference DB (REQUIRES DB MIGRATION)
 
 ## 8/22/23
 * Add db indices to optimize RNA data queries (REQUIRES DB MIGRATION)

reference_data/management/commands/update_gene_shet.py

@@ -0,0 +1,24 @@
+import logging
+from reference_data.management.commands.utils.update_utils import GeneCommand, ReferenceDataHandler
+from reference_data.models import GeneShet
+
+logger = logging.getLogger(__name__)
+
+
+class ShetReferenceDataHandler(ReferenceDataHandler):
+
+    model_cls = GeneShet
+    # The .tsv file is generated from the Google Doc at https://docs.google.com/spreadsheets/d/1enxGBWCAFBHdrRlqCj_ueleiDo9K9GWn/edit#gid=1146995171
+    # by downloading with a tsv format.
+    url = 'https://storage.googleapis.com/seqr-reference-data/gene_constraint/shet_Zeng(2023).xlsx%20-%20All%20scores-for%20gene%20page.tsv'
+
+    @staticmethod
+    def parse_record(record):
+        yield {
+            'gene_id': record['ensg'],
+            'shet': float(record['post_mean (Shet)']),
+        }
+
+
+class Command(GeneCommand):
+    reference_data_handler = ShetReferenceDataHandler

reference_data/management/tests/update_gene_shet_tests.py

@@ -0,0 +1,20 @@
+from reference_data.models import GeneShet
+from reference_data.management.tests.test_utils import ReferenceDataCommandTestCase
+
+class UpdateGeneShetTest(ReferenceDataCommandTestCase):
+    URL = 'https://storage.googleapis.com/seqr-reference-data/gene_constraint/shet_Zeng(2023).xlsx%20-%20All%20scores-for%20gene%20page.tsv'
+    DATA = [
+        'ensg	hgnc	post_mean (Shet)\n',
+        'ENSG00000223972	HGNC:37225	3.01E-05\n',
+        'ENSG00000227233	HGNC:26441	4.85E-05\n',
+        'ENSG00000243485	HGNC:4013	5.08E-05\n',
+    ]
+
+    def test_update_gene_cn_sensitivity_command(self):
+        self._test_update_command('update_gene_shet', 'GeneShet', created_records=2)
+
+        self.assertEqual(GeneShet.objects.count(), 2)
+        record = GeneShet.objects.get(gene__gene_id='ENSG00000223972')
+        self.assertEqual(record.shet, 3.01E-05)
+        record = GeneShet.objects.get(gene__gene_id='ENSG00000243485')
+        self.assertEqual(record.shet, 5.08E-05)

reference_data/migrations/0022_geneshet.py

@@ -0,0 +1,22 @@
+# Generated by Django 3.2.20 on 2023-08-25 14:33
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('reference_data', '0021_auto_20221031_2049'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='GeneShet',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('shet', models.FloatField()),
+                ('gene', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='reference_data.geneinfo')),
+            ],
+        ),
+    ]

reference_data/models.py

@@ -161,6 +161,15 @@ class Meta:
         json_fields = ['pHI', 'pTS']
 
 
+class GeneShet(models.Model):
+    gene = models.ForeignKey(GeneInfo, on_delete=models.CASCADE)
+
+    shet = models.FloatField()
+
+    class Meta:
+        json_fields = ['shet']
+
+
 class Omim(models.Model):
     MAP_METHOD_CHOICES = (
         ('1', 'the disorder is placed on the map based on its association with a gene, but the underlying defect is not known.'),

seqr/fixtures/reference_data.json

@@ -1167,6 +1167,14 @@
         "pHI": 0.90576,
         "pTS": 0.7346
     }
+},
+{
+    "model": "reference_data.geneshet",
+    "pk": 1,
+    "fields": {
+        "gene": 1,
+        "shet": 0.90576
+    }
 },
     {
     "model": "reference_data.dbnsfpgene",