#480 - store API responses so we can check lengths

genes/hgvs.py

@@ -756,7 +756,7 @@ def _variant_to_hgvs(self, variant: Variant, transcript_name=None) -> Tuple[HGVS
                     raise ValueError(f"Could not convert {variant} to HGVS - tried: {attempts}")
             else:
                 # No methods tried, mustn't have had any transcripts
-                raise TranscriptVersion.raise_bad_or_missing_transcript(self.genome_build, transcript_name)
+                raise TranscriptVersion.raise_bad_or_missing_transcript(transcript_name)
         else:
             hgvs_name = pyhgvs.variant_to_hgvs_name(chrom, offset, ref, alt, self.genome_build.genome_fasta.fasta,
                                                     transcript=None, max_allele_length=sys.maxsize)

genes/management/commands/import_refseq_transcript_fasta.py

@@ -0,0 +1,59 @@
+import logging
+from collections import defaultdict
+
+from Bio import SeqIO
+from django.core.management import BaseCommand
+from django.db.models import QuerySet
+
+from genes.models import TranscriptVersionInfo, TranscriptVersionInfoFastaFileImport, TranscriptVersion, Transcript
+from genes.models_enums import AnnotationConsortium
+from library.file_utils import file_md5sum, open_handle_gzip
+
+
+
+
+class Command(BaseCommand):
+
+    def add_arguments(self, parser):
+        parser.add_argument('--overwrite', action='store_true', help='Delete and replace fasta import with same md5sum')
+        parser.add_argument('filename')
+
+    def handle(self, *args, **options):
+        filename = options["filename"]
+        overwrite = options["overwrite"]
+
+        md5_hash = file_md5sum(filename)
+        if existing_import := TranscriptVersionInfoFastaFileImport.objects.filter(md5_hash=md5_hash).first():
+            if overwrite:
+                print(f"Deleting existing TranscriptVersionInfos for fasta import {md5_hash}")
+                existing_import.delete()
+            else:
+                raise ValueError(f"Fasta import {md5_hash} exists, use --overwrite to delete old data")
+
+        known_transcripts = set(Transcript.objects.all().values_list("identifier", flat=True))
+        if not known_transcripts:
+            raise ValueError("No transcripts! Insert them first!")
+
+        fasta_import = TranscriptVersionInfoFastaFileImport.objects.create(md5_hash=md5_hash,
+                                                                           annotation_consortium=AnnotationConsortium.REFSEQ,
+                                                                           filename=filename)
+        skipped_transcripts = 0
+        records = []
+        with open_handle_gzip(filename, "rt") as f:
+            for record in SeqIO.parse(f, "fasta"):
+                transcript_id, version = TranscriptVersion.get_transcript_id_and_version(record.id)
+                if transcript_id not in known_transcripts:
+                    skipped_transcripts += 1
+                    continue
+
+                tvi = TranscriptVersionInfo(transcript_id=transcript_id, version=version,
+                                            fasta_import=fasta_import,
+                                            sequence=str(record.seq), length=len(record.seq))
+                records.append(tvi)
+
+        print(f"Skipped {skipped_transcripts} transcripts not in our database")
+        if num_records := len(records):
+            print(f"Inserting {num_records} TranscriptVersionInfo records")
+            TranscriptVersionInfo.objects.bulk_create(records, ignore_conflicts=True, batch_size=2000)
+
+        TranscriptVersionInfo.set_transcript_version_alignment_gap_if_length_different(records)

genes/migrations/0039_transcriptversioninfo_transcriptversioninfofastafileimport.py

@@ -0,0 +1,47 @@
+# Generated by Django 3.2.6 on 2021-09-14 02:01
+
+from django.db import migrations, models
+import django.db.models.deletion
+import django_extensions.db.fields
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('genes', '0038_lrgrefseqgene'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='TranscriptVersionInfoFastaFileImport',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', django_extensions.db.fields.CreationDateTimeField(auto_now_add=True, verbose_name='created')),
+                ('modified', django_extensions.db.fields.ModificationDateTimeField(auto_now=True, verbose_name='modified')),
+                ('md5_hash', models.CharField(max_length=32, unique=True)),
+                ('annotation_consortium', models.CharField(choices=[('R', 'RefSeq'), ('E', 'Ensembl')], max_length=1)),
+                ('filename', models.TextField()),
+            ],
+            options={
+                'get_latest_by': 'modified',
+                'abstract': False,
+            },
+        ),
+        migrations.CreateModel(
+            name='TranscriptVersionInfo',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', django_extensions.db.fields.CreationDateTimeField(auto_now_add=True, verbose_name='created')),
+                ('modified', django_extensions.db.fields.ModificationDateTimeField(auto_now=True, verbose_name='modified')),
+                ('version', models.IntegerField()),
+                ('api_response', models.TextField(null=True)),
+                ('sequence', models.TextField()),
+                ('length', models.IntegerField()),
+                ('fasta_import', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='genes.transcriptversioninfofastafileimport')),
+                ('transcript', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='genes.transcript')),
+            ],
+            options={
+                'unique_together': {('transcript', 'version')},
+            },
+        ),
+    ]