biocommons.anyvar 1.0.0rc3

AnyVar provides Python and REST interfaces to validate, normalize, generate identifiers, and register biological sequence variation according to the GA4GH Variation Representation standards.

AnyVar - lightweight and portable variation storage and retrieval

AnyVar enables registration, lookup, and search of genetic variants across a distributed genomic resource network. Its goals are to:

• Provide an open source, off-the-shelf solution that lowers the technical barriers for genomic data resources to comprehensively describe and search genomic variants
• Support a broad range of query modes, including VRS ID lookups, HGVS expressions, gene-based searches, and genomic ranges
• Translate community nomenclatures and conventions into a universal model for variant representation
• Provide a community-driven, extensible platform for shared conventions and policy to realize the above goals

Information

Latest Release

Development

Installation

Currently, AnyVar can be installed from GitHub:

pip install git+https://github.com/biocommons/anyvar

See the documentation for additional setup options and detailed instructions for initializing data dependencies.

Examples

Use the Python API to directly instantiate and query a local AnyVar instance:

>>> from anyvar.anyvar import AnyVar, create_storage, create_translator
>>> av = AnyVar(translator=create_translator(), object_store=create_storage())
>>> allele = Allele(**{"id": "ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU", "digest": "K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU", "location": {"id": "ga4gh:SL.aCMcqLGKClwMWEDx3QWe4XSiGDlKXdB8", "digest": "aCMcqLGKClwMWEDx3QWe4XSiGDlKXdB8", "end": 87894077, "start": 87894076, "sequenceReference": {"refgetAccession": "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB"}}, "state": {"sequence": "T", "type": "LiteralSequenceExpression"}})
>>> av.put_object(allele)
'ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU'
>>> av.get_object("ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU")
Allele(id='ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU', type='Allele', name=None, description=None, aliases=None, extensions=None, digest='K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU', expressions=None, location=SequenceLocation(id='ga4gh:SL.aCMcqLGKClwMWEDx3QWe4XSiGDlKXdB8', type='SequenceLocation', name=None, description=None, aliases=None, extensions=None, digest='aCMcqLGKClwMWEDx3QWe4XSiGDlKXdB8', sequenceReference=SequenceReference(id=None, type='SequenceReference', name=None, description=None, aliases=None, extensions=None, refgetAccession='SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB', residueAlphabet=None, circular=None, sequence=None, moleculeType=None), start=87894076, end=87894077, sequence=None), state=LiteralSequenceExpression(id=None, type='LiteralSequenceExpression', name=None, description=None, aliases=None, extensions=None, sequence=sequenceString(root='T')))

Or issue a request against a live HTTP endpoint:

>>> import requests
>>> response = requests.put("http://localhost:8000/variation", json={"definition": "NC_000010.11:g.87894077C>T"})
>>> response.json()
{'messages': [], 'object': {'id': 'ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU', 'type': 'Allele', 'digest': 'K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU', 'location': {'id': 'ga4gh:SL.01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy', 'type': 'SequenceLocation', 'digest': '01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy', 'sequenceReference': {'type': 'SequenceReference', 'refgetAccession': 'SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB'}, 'start': 87894076, 'end': 87894077}, 'state': {'type': 'LiteralSequenceExpression', 'sequence': 'T'}}, 'object_id': 'ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU'}
>>> response = requests.get("http://localhost:8000/variation/ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU")
>>> response.json()
{'messages': [], 'data': {'id': 'ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU', 'type': 'Allele', 'digest': 'K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU', 'location': {'id': 'ga4gh:SL.aCMcqLGKClwMWEDx3QWe4XSiGDlKXdB8', 'type': 'SequenceLocation', 'digest': 'aCMcqLGKClwMWEDx3QWe4XSiGDlKXdB8', 'sequenceReference': {'type': 'SequenceReference', 'refgetAccession': 'SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB'}, 'start': 87894076, 'end': 87894077}, 'state': {'type': 'LiteralSequenceExpression', 'sequence': 'T'}}}

Feedback and contributing

We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The documentation contains guidance for submitting feedback and contributing new code.