...
Using the Python client (PyCellBase)
A wrapper method is implemented within the VariantClient object for performing variant annotation. Thus, variant annotation can be carried out by simply calling this "get_annotation" method:
Code Block | ||
---|---|---|
| ||
from pycellbase.cbconfig import ConfigClient
from pycellbase.cbclient import CellBaseClient
cbc = CellBaseClient(cc)
result = variant_client.get_annotation("19:45411941:T:C,1:69585:TGAGGTCGATAGTTTTTA:-,14:38679764:-:GATCTGAGAAGNGGAANANAAGGG,19:33167329:AC:TT,22:16328960-16344095:<CN5>,22:16328960-16344095:<CN1>,22:16328960-16344095:<CNV>,22:16328960-16344095:<DEL>,22:16328960-16344095:<DUP>,22:16328960-16344095:<INV>")
len(result)
10
result[8]["result"][0]
{u'alternate': u'<DUP>',
u'chromosome': u'22',
u'consequenceTypes': [{u'biotype': u'unprocessed_pseudogene',
u'ensemblGeneId': u'ENSG00000234381',
u'ensemblTranscriptId': u'ENST00000435410',
u'geneName': u'MED15P7',
u'sequenceOntologyTerms': [{u'accession': u'SO:0001889',
u'name': u'transcript_amplification'}],
u'strand': u'+',
u'transcriptAnnotationFlags': [u'basic']},
{u'biotype': u'unprocessed_pseudogene',
u'ensemblGeneId': u'ENSG00000224435',
u'ensemblTranscriptId': u'ENST00000426025',
u'geneName': u'NF1P6',
u'sequenceOntologyTerms': [{u'accession': u'SO:0001636',
u'name': u'2KB_upstream_variant'}],
u'strand': u'+',
u'transcriptAnnotationFlags': [u'basic']},
{u'sequenceOntologyTerms': [{u'accession': u'SO:0001566',
u'name': u'regulatory_region_variant'}]}],
...
...
...
result[8]["result"][0]["consequenceTypes"]
[{u'biotype': u'unprocessed_pseudogene',
u'ensemblGeneId': u'ENSG00000234381',
u'ensemblTranscriptId': u'ENST00000435410',
u'geneName': u'MED15P7',
u'sequenceOntologyTerms': [{u'accession': u'SO:0001889',
u'name': u'transcript_amplification'}],
u'strand': u'+',
u'transcriptAnnotationFlags': [u'basic']},
{u'biotype': u'unprocessed_pseudogene',
u'ensemblGeneId': u'ENSG00000224435',
u'ensemblTranscriptId': u'ENST00000426025',
u'geneName': u'NF1P6',
u'sequenceOntologyTerms': [{u'accession': u'SO:0001636',
u'name': u'2KB_upstream_variant'}],
u'strand': u'+',
u'transcriptAnnotationFlags': [u'basic']},
{u'sequenceOntologyTerms': [{u'accession': u'SO:0001566',
u'name': u'regulatory_region_variant'}]}]
|
Using the R client (cellbaseR)
...