get_wastewater_lineages¶
- outbreak_data.get_wastewater_lineages(input_df, **req_args)¶
Add wastewater demix results to a DataFrame containing sample IDs.
- Parameters
input_df -- DataFrame containing metadata.
- Returns
The input dataframe joined with lineage data columns.
- Parameter example
{ 'input_df': pd.DataFrame({'sra_accession': ['SRR26963071', 'SRR25666039']}), 'server': 'dev.outbreak.info' }
Note that this function is used in conjunction with get_wastewater_mutations.
Example Usage
Find lineages of samples associated with A --> G base mutations at genome position 1003:
# Collect wastewater mutation data
>>> samples = outbreak_data.get_wastewater_samples_by_mutation(site=1003, alt_base='G', server='dev.outbreak.info')
>>> outbreak_data.get_wastewater_lineages(samples, server='dev.outbreak.info')
alt_base depth prevalence_x ref_base site \
mutation lineage
1003 AND alt_base:G CK.1.1.1 G 51 0.038088 A 1003
CL.1.3 G 51 0.038088 A 1003
DV.1.1 G 51 0.038088 A 1003
HW.1 G 51 0.038088 A 1003
XBJ.4 G 51 0.038088 A 1003
... ... ... ... ... ...
JR.1.1.1 G 23 0.273810 A 1003
JY.1.1 G 23 0.273810 A 1003
KE.3 G 23 0.273810 A 1003
KT.1.1 G 23 0.273810 A 1003
XBB.1.24 G 23 0.273810 A 1003
sra_accession query coverage \
mutation lineage
1003 AND alt_base:G CK.1.1.1 SRR21864715 SRR21864715 97.555429
CL.1.3 SRR21864715 SRR21864715 97.555429
DV.1.1 SRR21864715 SRR21864715 97.555429
HW.1 SRR21864715 SRR21864715 97.555429
XBJ.4 SRR21864715 SRR21864715 97.555429
... ... ... ...
JR.1.1.1 SRR25022780 SRR25022780 9.848510
JY.1.1 SRR25022780 SRR25022780 9.848510
KE.3 SRR25022780 SRR25022780 9.848510
KT.1.1 SRR25022780 SRR25022780 9.848510
XBB.1.24 SRR25022780 SRR25022780 9.848510
crumbs \
mutation lineage
1003 AND alt_base:G CK.1.1.1 ;B;B.1;B.1.1;B.1.1.529;B.1.1.529.5;B.1.1.529.5...
CL.1.3 ;B;B.1;B.1.1;B.1.1.529;B.1.1.529.5;B.1.1.529.5...
DV.1.1 ;B;B.1;B.1.1;B.1.1.529;B.1.1.529.2;B.1.1.529.2...
HW.1 ;XBC;XBC.1;XBC.1.6;XBC.1.6.3;XBC.1.6.3.1;HW;HW.1;
XBJ.4 ;XBJ;XBJ.4;
... ...
JR.1.1.1 ;XBB;XBB.1;XBB.1.9;XBB.1.9.2;XBB.1.9.2.5;XBB.1...
JY.1.1 ;XBB;XBB.2;XBB.2.3;XBB.2.3.19;XBB.2.3.19.1;XBB...
KE.3 ;XBB;XBB.1;XBB.1.19;XBB.1.19.1;XBB.1.19.1.5;XB...
KT.1.1 ;XBB;XBB.2;XBB.2.3;XBB.2.3.10;XBB.2.3.10.1;XBB...
XBB.1.24 ;XBB;XBB.1;XBB.1.24;
prevalence_y spike_coverage
mutation lineage
1003 AND alt_base:G CK.1.1.1 0.000530 98.874935
CL.1.3 0.000550 98.874935
DV.1.1 0.000106 98.874935
HW.1 0.000220 98.874935
XBJ.4 0.000288 98.874935
... ... ...
JR.1.1.1 0.131121 3.218210
JY.1.1 0.100538 3.218210
KE.3 0.008403 3.218210
KT.1.1 0.238095 3.218210
XBB.1.24 0.018568 3.218210
[6085 rows x 11 columns]