mutation_details

outbreak_data.mutation_details(mutations, **req_args)

Get details of one or more mutations from clinical data.

Parameters

mutations -- Mutation or list of mutations of interest.

Returns

A pandas dataframe with one row per mutation.

Parameter example

{'mutations':'s:e484*'}

Get details on all mutations with "E484" in the name:

  >>> df = outbreak_data.mutation_details('*e484*')
  >>> df

                 type gene ref_codon    pos alt_codon  is_synonymous ref_aa  \
mutation
S:E484L   substitution    S       GAA  23012       CTT          False      E
S:E484A   substitution    S       GAA  23013       GCC          False      E
S:E484R   substitution    S       GAA  23012       AGG          False      E
S:E484V   substitution    S       GAA  23012       GTG          False      E
S:E484T   substitution    S       GAA  23012       ACA          False      E
S:E484D   substitution    S       GAA  23012       GAC          False      E
S:E484H   substitution    S       GAA  23013       CAT          False      E
S:E484K   substitution    S       GAA  23013       AAG          False      E
S:E484Q   substitution    S       GAA  23011       CAA          False      E
S:E484I   substitution    S       GAA  23011       ATA          False      E

          codon_num alt_aa
mutation
S:E484L         484      L
S:E484A         484      A
S:E484R         484      R
S:E484V         484      V
S:E484T         484      T
S:E484D         484      D
S:E484H         484      H
S:E484K         484      K
S:E484Q         484      Q
S:E484I         484      I