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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

language	py

>>> 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'}]}],
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>>> 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'}]}]

As with any other method offered by the client, additional query parameters can be passed to refine the annotation, e.g. include, exclude, etc. Available parameters can be found in the Swagger documentation: http://bioinfo.hpc.cam.ac.uk/cellbase/webservices

Note that a normalize parameter can be activated enabling, for example, to provide reference and alternate strings in a VCF-like format.

Using the R client (cellbaseR)

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Using the R client (cellbaseR)