wildcard_lineage

outbreak_data.wildcard_lineage(search, **req_args)

Find pango lineages via wildcard search.

Parameters

search -- A query string for the lineage name; asterisks treated as wildcards.

Returns

A pandas dataframe containing matching lineages and clinical sequence counts.

Parameter example

{ 'search': '.86.' }

Example Usage

List all known lineages that start with 'g':

>>> df = outbreak_data.wildcard_lineage('g*')
>>> df

        total_count
name
gk.1.1         5683
gj.1.2         5610
ge.1           4469
gs.4.1         4368
gk.1           1777
...             ...
ga.7              1
ga.7.2            1
gd.3              1
gl.2              1
gy.2              1

[156 rows x 1 columns]

Find lineages that contain '.86':

>>> df = outbreak_data.wildcard_lineage('*.86*')
>>> df

            total_count
name
ba.2.86.1         10989
b.1.177.86         5498
ay.86              1105
ba.2.86             995
ba.2.86.3           366
ba.2.86.2           323
xbb.1.5.86          170
ba.2.86.5            38
b.1.1.86             26
ba.2.86.4            10