col_test_performed_desc

transform.col_test_performed_desc(wdrs_test_perf_col: str)

WDRS Test Performed Description

Usage

The function can be called into a .with_columns() statement. It will reference the dataframe’s status column and output a cleaned version of it.

Parameters

wdrs_test_perf_col : str

test performed column

Examples

import polars as pl
import wadoh_subtyping.transform as tf
from wadoh_raccoon.utils import helpers

df = pl.DataFrame({
    "ResultTextConclusion": [
        "Influenza A(2009 H1N1) virus detected by RT-PCR {65}", 
        "Influenza B/Victoria lineage detected by RT-PCR {91}", 
        "Inconclusive - sample below limit of detection of test {61}",
        "Influenza B virus detected by RT-PCR {59}"
    ]
})

# run the function
df = (
    df
    .with_columns(
        TEST_PERFORMED_DESC=tf.col_test_performed_desc(wdrs_test_perf_col='ResultTextConclusion')
    )
)

# here's a table of the results
helpers.gt_style(df_inp=df)

index	ResultTextConclusion	TEST_PERFORMED_DESC
0	Influenza A(2009 H1N1) virus detected by RT-PCR {65}	PCR/Nucleic Acid Test (NAT, NAAT, DNA)
1	Influenza B/Victoria lineage detected by RT-PCR {91}	PCR/Nucleic Acid Test (NAT, NAAT, DNA)
2	Inconclusive - sample below limit of detection of test {61}	None
3	Influenza B virus detected by RT-PCR {59}	PCR/Nucleic Acid Test (NAT, NAAT, DNA)

WDRS Variable Mapping

Below are all distinct options in WDRS for the WDRS_TEST_PERFORMED variable and how the values map to LIMS data.

LIMS-ResultTextConclusion	WDRS_TEST_PERFORMED
Inconclusive {50}	Direct fluorescent antibody (DFA) / Immunohistochemistry (IHC)
Influenza A virus detected by RT-PCR {58}	Manual Review
Influenza A(2009 H1N1) virus detected by RT-PCR {65}	PCR/Nucleic Acid Test (NAT, NAAT, DNA)
Influenza A(H3) virus detected by RT-PCR {64}	Rapid test (rapid EIA)
Influenza B virus detected by RT-PCR {59}	Viral culture (isolation)
	Other, specify