From 6b82e71ef4122688712d9b1ebad43ac74f8eeca2 Mon Sep 17 00:00:00 2001 From: TheMadBug Date: Tue, 9 Jul 2024 14:19:44 +1000 Subject: [PATCH] VCF parsing, handle new somatic review status of "criteria_provided,_multiple_submitters" --- ..._clinvar_clinvar_review_status_and_more.py | 28 +++++++++++++++++++ annotation/models/models_enums.py | 3 ++ 2 files changed, 31 insertions(+) create mode 100644 annotation/migrations/0109_alter_clinvar_clinvar_review_status_and_more.py diff --git a/annotation/migrations/0109_alter_clinvar_clinvar_review_status_and_more.py b/annotation/migrations/0109_alter_clinvar_clinvar_review_status_and_more.py new file mode 100644 index 000000000..d65df8fcf --- /dev/null +++ b/annotation/migrations/0109_alter_clinvar_clinvar_review_status_and_more.py @@ -0,0 +1,28 @@ +# Generated by Django 4.2.11 on 2024-07-09 04:17 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('annotation', '0108_one_off_vep_version_major_only'), + ] + + operations = [ + migrations.AlterField( + model_name='clinvar', + name='clinvar_review_status', + field=models.CharField(choices=[('N', 'No assertion provided'), ('C', 'No assertion criteria provided'), ('I', 'No interpretation for the single variant'), ('n', 'No Classification Provided'), ('f', 'No classifications from unflaggedrecords'), ('F', 'Criteria provided - conflicting interpretations'), ('S', 'Criteria provided - single submitter'), ('M', 'Criteria provided - multiple submitters w/no conflicts'), ('m', 'Criteria provided - multiple submitters'), ('E', 'Reviewed by expert panel'), ('P', 'Practice guideline')], max_length=1, null=True), + ), + migrations.AlterField( + model_name='clinvar', + name='oncogenic_review_status', + field=models.CharField(choices=[('N', 'No assertion provided'), ('C', 'No assertion criteria provided'), ('I', 'No interpretation for the single variant'), ('n', 'No Classification Provided'), ('f', 'No classifications from unflaggedrecords'), ('F', 'Criteria provided - conflicting interpretations'), ('S', 'Criteria provided - single submitter'), ('M', 'Criteria provided - multiple submitters w/no conflicts'), ('m', 'Criteria provided - multiple submitters'), ('E', 'Reviewed by expert panel'), ('P', 'Practice guideline')], max_length=1, null=True), + ), + migrations.AlterField( + model_name='clinvar', + name='somatic_review_status', + field=models.CharField(choices=[('N', 'No assertion provided'), ('C', 'No assertion criteria provided'), ('I', 'No interpretation for the single variant'), ('n', 'No Classification Provided'), ('f', 'No classifications from unflaggedrecords'), ('F', 'Criteria provided - conflicting interpretations'), ('S', 'Criteria provided - single submitter'), ('M', 'Criteria provided - multiple submitters w/no conflicts'), ('m', 'Criteria provided - multiple submitters'), ('E', 'Reviewed by expert panel'), ('P', 'Practice guideline')], max_length=1, null=True), + ), + ] diff --git a/annotation/models/models_enums.py b/annotation/models/models_enums.py index 145d79af5..058bb34b3 100644 --- a/annotation/models/models_enums.py +++ b/annotation/models/models_enums.py @@ -169,6 +169,7 @@ class ClinVarReviewStatus(models.TextChoices): CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS = "F", "Criteria provided - conflicting interpretations" CRITERIA_PROVIDED_SINGLE_SUBMITTER = "S", "Criteria provided - single submitter" CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = "M", "Criteria provided - multiple submitters w/no conflicts" + CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS = "m", "Criteria provided - multiple submitters" # somatic only REVIEWED_BY_EXPERT_PANEL = "E", "Reviewed by expert panel" PRACTICE_GUIDELINE = "P", "Practice guideline" @@ -180,6 +181,7 @@ class ClinVarReviewStatus(models.TextChoices): CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS[0]: 1, CRITERIA_PROVIDED_SINGLE_SUBMITTER[0]: 1, CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS[0]: 2, + CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS[0]: 2, REVIEWED_BY_EXPERT_PANEL[0]: 3, PRACTICE_GUIDELINE[0]: 4, }) @@ -194,6 +196,7 @@ class ClinVarReviewStatus(models.TextChoices): 'criteria_provided,_conflicting_interpretations': CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS[0], 'criteria_provided,_conflicting_classifications': CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS[0], 'criteria_provided,_single_submitter': CRITERIA_PROVIDED_SINGLE_SUBMITTER[0], + 'criteria_provided,_multiple_submitters': CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS[0], # new for somatic 'criteria_provided,_multiple_submitters,_no_conflicts': CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS[0], 'reviewed_by_expert_panel': REVIEWED_BY_EXPERT_PANEL[0], 'practice_guideline': PRACTICE_GUIDELINE[0],