sequence_counts(location, cumulative, sub_admin)

outbreak_data.sequence_counts(location=None, cumulative=None, sub_admin=None, server='api.outbreak.info')

Returns number of sequences per day by location

Arguments:

location:

(Optional). If not specified, the global total counts are returned.

cumulative:

(Optional). If true returns the cumulative number of sequences till date.

subadmin:

(Optional). If true and cumulative=true, returns the cumulative number of sequences for the immedaite lower admin level.

return:

A pandas dataframe.

Example usage:

1. Get number of daily sequence counts in the US:

   df = od.sequence_counts('USA')
   print(df)
   

Output

            Key        Values
 0       mutation   ORF1b:P314L
 1      alt_codon           CTT
 2  is_synonymous         False
 3      codon_num           314
 4      ref_codon           CCT
 5           gene         ORF1b
 6            pos         14407
 7         alt_aa             L
 8         ref_aa             P
 9           type  substitution

2. Get total number of sequence counts

   df = od.sequence_counts(‘USA’, cumulative=True) print(df)

Output

               Values
 total_count  4617418