get_wastewater_samples_by_mutation¶
- outbreak_data.get_wastewater_samples_by_mutation(site, alt_base=None, min_prevalence=0.01, **req_args)¶
Get IDs of wastewater samples containing a mutation at a certain site.
- Parameters
site -- Positive integer representing the base pair index of mutations of interest.
alt_base -- The new base at that site (from ['G', 'A', 'T', 'C']).
min_prevalence -- The minimum prevalence necessary for a sample to be considered to contain a mutation.
- Returns
A pandas series containing IDs of samples found to contain matching mutations.
- Parameter example
{ 'site': 1003, 'alt_base': 'G', 'server': 'dev.outbreak.info' }
Example Usage
Find wastewater samples with A --> G base mutations at position 1003:
>>> outbreak_data.get_wastewater_samples_by_mutation(site=1003, alt_base='G', server='dev.outbreak.info')
alt_base depth prevalence ref_base site sra_accession
mutation
1003 AND alt_base:G G 51 0.038088 A 1003 SRR21864715
1003 AND alt_base:G G 37 0.016364 A 1003 SRR26898771
1003 AND alt_base:G G 17489 0.267682 A 1003 SRR22275905
1003 AND alt_base:G G 2708 0.024436 A 1003 SRR27050417
1003 AND alt_base:G G 1398 0.677654 A 1003 SRR26979184
1003 AND alt_base:G G 51 0.015450 A 1003 SRR21662569
1003 AND alt_base:G G 17049 0.355165 A 1003 SRR24899723
1003 AND alt_base:G G 119 0.010776 A 1003 SRR21492603
1003 AND alt_base:G G 145 0.018189 A 1003 SRR26111437
1003 AND alt_base:G G 254 0.072884 A 1003 SRR24837595
1003 AND alt_base:G G 20 0.256410 A 1003 SRR26776578
... ... ... ... ...
[45 rows x 6 columns]