| 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 |
| # /// script | |
| # dependencies = [ | |
| # "requests", | |
| # ] | |
| # /// | |
| import os | |
| from pathlib import Path | |
| from datetime import datetime | |
| import csv | |
| import requests |
| { | |
| "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", |
| { | |
| "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" | |
| }, |
| { | |
| "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", |
| In [21]: input_data = { | |
| ...: "location": { | |
| ...: "end": 87894077, | |
| ...: "start": 87894076, | |
| ...: "sequenceReference": { | |
| ...: "refgetAccession": "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB", | |
| ...: "type": "SequenceReference" | |
| ...: }, | |
| ...: }, | |
| ...: "state": { |
| 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, |
| civic.eid:3811 can be loaded. | |
| civic.eid:229 can be loaded. | |
| civic.eid:4291 can be loaded. | |
| civic.eid:4290 can be loaded. | |
| civic.eid:4285 can be loaded. | |
| civic.eid:4265 can be loaded. | |
| civic.eid:885 can be loaded. | |
| civic.eid:2994 can be loaded. | |
| civic.aid:5 can be loaded. | |
| civic.eid:2621 can be loaded. |
| [ | |
| { | |
| "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}", |
uv is a Python tool for managing dependencies, builds, and runtimes. Inspired by major players in other languages like cargo and npm. It should further simplify the hassle of dealing with Python runtimes and environments and I would strongly recommend switching over to it.
Get rid of pyenv