adamds / biomine Goto Github PK

When using splitSNVHGVSc with override = True, it does not consider on which strand the gene is located. In case of the - strand it should reverse complement ref and alt.

Error:
line 248, in trySubmit
print( "BioMine::webapi::ensembl::ensemblapi::trySubmit Error: failed to query due to " + str( self.status_code ) + ": " + self.reason )
AttributeError: 'ensemblapi' object has no attribute 'status_code'

Possible solution:
change to self.response.status_code & self.response.reason

Also:
change behavior to try again if exceeds request frequency limit instead of erring out immediately

The current software seems to be unable to handle deletions insertion events.

biomine::variant::mafvariant Warning: could not find amino acid change or intronic change
  Hint: Is the input amino acid change column correct?
    Problem variant:  BRCA2:13:32319296-32319298AAGAATT>A::NM_000059.3:c.delAAGAATTinsA::NP_000050.2:p.  --  p.Glu97_Leu98del