James Stevenson jsstevenson

bioinformatics software developer @GenomicMedLab

jsstevenson / gist:a5de75d9764082209b69f174dd8a557c

Created January 30, 2026 01:47

vaf_cbioportal_example_20260129.json

	{
	"type": "TumorVariantFrequencyStudyResult",
	"id": "<figure out an ID rule>",
	"focusVariant": "ga4gh:VA.kNnN0j0CvPaXeJyCmDFmTATjIwjPrJLn", // pretend there's a whole variation here. or catvar?
	"affectedSampleCount": 2, // total # of samples in study w/ allele
	"totalSampleCount": 34, // total # of samples in study
	"affectedFrequency": 0.058824,
	"sampleGroup": {
	"id": "all_stjude_2015",
	"label": "all_stjude_2015",

jsstevenson / gks_usage_stats_20260121.csv

Last active January 22, 2026 03:11

usage stats snapshot for gks/biocommons computational tools

name	github_url	gh_stars	gh_forks	gh_participants	pypi_name	last_month_pypi_downloads	dh_pull_count	total_ghcr_downloads
VRS	https://github.com/ga4gh/vrs	94	38	58
VA-Spec	https://github.com/ga4gh/va-spec	26	7	39
Cat-VRS	https://github.com/ga4gh/cat-vrs	5	4	16
Metaschema Processor	https://github.com/ga4gh/gks-metaschema	0	1	9	ga4gh.gks.metaschema	601
vrs-python	https://github.com/ga4gh/vrs-python	61	39	48	ga4gh.vrs	19332	14
cat-vrs-python	https://github.com/ga4gh/cat-vrs-python	1	4	5	ga4gh.cat-vrs	3786
va-spec-python	https://github.com/ga4gh/va-spec-python	2	1	4	ga4gh.va-spec	3852
seqrepo	https://github.com/biocommons/biocommons.seqrepo	47	35	54	biocommons.seqrepo	67234	26225
hgvs	https://github.com/biocommons/hgvs	287	98	141	hgvs	61932	245

jsstevenson / software_stats.py

Last active January 22, 2026 04:41

simple script to grab snapshot of basic usage stats for specific libs of interest

	# /// script
	# dependencies = [
	# "requests",
	# ]
	# ///
	import os
	from pathlib import Path
	from datetime import datetime
	import csv
	import requests

jsstevenson / metakb_moa_cdm_20260108.json

Created January 8, 2026 20:47

	{
	"assertions":{
	"id":"metakb:id that sums up the proposition parts",
	"type":"Statement",
	"specifiedBy":{
	"id":"metakb.method:2026",
	"type":"Method",
	"name":"MetaKB (2026)",
	"reportedIn":{
	"type":"Document",

jsstevenson / metakb_grouped_statement_example.json

Created December 19, 2025 03:17

	{
	"id": "metakb.placeholder:1",
	"type": "Statement",
	"specifiedBy": { "id": "placeholder" },
	"proposition": {
	"type": "VariantTherapeuticResponseProposition",
	"subjectVariant": {
	"id": "catvar equivalent of GA4GH.VAxxxx from below, we can come up with something",
	"content": "the catvar etc"
	},

jsstevenson / moa_featurecontextconstraint_example.json

Last active December 1, 2025 18:49

	{
	"id": "moa.assertion:74",
	"type": "Statement",
	"description": "Secondary mutations in BCR-ABL may suggest resistance to imatinib in CML.",
	"specifiedBy": {
	"id": "moa.method:2021",
	"type": "Method",
	"name": "MOAlmanac (2021)",
	"reportedIn": {
	"type": "Document",

jsstevenson / gist:39d5de8428bc3bc450987530945ee2b8

Created November 21, 2025 21:09

	In [21]: input_data = {
	...: "location": {
	...: "end": 87894077,
	...: "start": 87894076,
	...: "sequenceReference": {
	...: "refgetAccession": "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB",
	...: "type": "SequenceReference"
	...: },
	...: },
	...: "state": {

jsstevenson / 2025-10-03-stack trace

Created October 3, 2025 18:24

	self = <botocore.awsrequest.AWSHTTPConnectionPool object at 0x11195bf50>, conn = <botocore.awsrequest.AWSHTTPConnection object at 0x1119d4b90>
	method = 'POST', url = '/Execute'
	body = b'{"sql": "DROP DATABASE IF EXISTS `varcat`;", "secretArn": "arn:aws:secretsmanager:us-east-1:123456789012:secret:dummy", "resourceArn": "arn:aws:rds:us-east-1:123456789012:cluster:dummy"}'
	headers = {'Content-Type': b'application/json', 'User-Agent': b'Boto3/1.40.42 md/Botocore#1.40.42 ua/2.1 os/macos#24.6.0 md/arch...vocation-id': b'e1996f6f-cd92-4adf-9410-7fcac12dce9e', 'amz-sdk-request': b'attempt=5; max=5', 'Content-Length': '186'}
	retries = Retry(total=False, connect=None, read=None, redirect=0, status=None), timeout = Timeout(connect=60, read=60, total=None)
	chunked = False, response_conn = <botocore.awsrequest.AWSHTTPConnection object at 0x1119d4b90>, preload_content = False
	decode_content = False, enforce_content_length = True

	def _make_request(
	self,

jsstevenson / metakb_assertion_ingest_fails.txt

Last active August 30, 2025 01:54

jsstevenson / metakb_strenght_nodes.json

Created August 28, 2025 20:47

MetaKB Strength nodes

	[
	{
	"n": {
	"identity": 1625,
	"labels": [
	"Strength"
	],
	"properties": {
	"mappings": "[{\"id\":null,\"extensions\":null,\"coding\":{\"id\":null,\"extensions\":null,\"name\":\"preclinical evidence\",\"system\":\"https://go.osu.edu/evidence-codes\",\"systemVersion\":null,\"code\":\"e000009\",\"iris\":null},\"relation\":\"exactMatch\"}]",
	"primary_coding": "{\"id\":null,\"extensions\":null,\"name\":null,\"system\":\"https://civic.readthedocs.io/en/latest/model/evidence/level.html\",\"systemVersion\":null,\"code\":\"D\",\"iris\":null}",