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Merge pull request #39 from dholab/proposals
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Addition of the latest positivity results as of 2024-06-25
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@nrminor
nrminor authored Jun 25, 2024
2 parents 1f2d7df + 6e73239 commit c4b7283
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24 changes: 12 additions & 12 deletions DETECTION_RESULTS.tsv
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Expand Up @@ -74,15 +74,15 @@ dholab_30260_10 dholab_carton_0052 2024-06-05 2024-06-18 qPCR DHO_CN_HPAIspec
dholab_30260_11 dholab_carton_0053 2024-06-05 2024-06-28 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE IN dholab 2024-06-14
dholab_30260_12 dholab_carton_0054 2024-06-05 2024-06-22 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE TX dholab 2024-06-14
dholab_30260_13 dholab_carton_0055 2024-06-05 2024-06-20 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-14
dholab_30260_14 dholab_carton_0056 2024-06-05 2024-06-18 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-14
dholab_30303_01 dholab_carton_0057 2024-06-18 07-31-2024 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE MN dholab 2024-06-18
dholab_30303_02 dholab_carton_0058 2024-06-18 07-08-2024 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE IN dholab 2024-06-18
dholab_30303_03 dholab_carton_0059 2024-06-18 06-25-20224 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-18
dholab_30303_04 dholab_carton_0060 2024-06-18 07-03-2024 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-18
dholab_30303_05 dholab_carton_0061 2024-06-18 06-18-2024 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-18
dholab_30303_06 dholab_carton_0062 2024-06-18 07-03-2024 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-18
dholab_30303_07 dholab_carton_0063 2024-06-18 08-29-2024 qPCR 33 DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE MI dholab 2024-06-18
dholab_30303_08 dholab_carton_0064 2024-06-18 07-15-2024 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE IL dholab 2024-06-18
dholab_30303_09 dholab_carton_0065 2024-06-18 08-23-2024 qPCR 29.89 DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE CO dholab 2024-06-18
dholab_30303_10 dholab_carton_0066 2024-06-18 07-01-0145 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE IA dholab 2024-06-18
dholab_30303_11 dholab_carton_0067 2024-06-18 07-22-2024 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE KY dholab 2024-06-18
dholab_30260_14 dholab_carton_0056 2024-06-05 2024-06-18 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-14
dholab_30303_01 dholab_carton_0057 2024-06-17 2024-07-31 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE MN dholab 2024-06-18
dholab_30303_02 dholab_carton_0058 2024-06-17 2024-07-08 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE IN dholab 2024-06-18
dholab_30303_03 dholab_carton_0059 2024-06-17 2024-06-25 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-18
dholab_30303_04 dholab_carton_0060 2024-06-17 2024-07-03 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-18
dholab_30303_05 dholab_carton_0061 2024-06-17 2024-06-18 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-18
dholab_30303_06 dholab_carton_0062 2024-06-17 2024-07-03 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE WI dholab 2024-06-18
dholab_30303_07 dholab_carton_0063 2024-06-17 2024-08-29 qPCR 33 DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE MI dholab 2024-06-18
dholab_30303_08 dholab_carton_0064 2024-06-17 2024-07-15 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE IL dholab 2024-06-18
dholab_30303_09 dholab_carton_0065 2024-06-17 2024-08-23 qPCR 29.89 DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE CO dholab 2024-06-18
dholab_30303_10 dholab_carton_0066 2024-06-17 2024-07-01 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE IA dholab 2024-06-18
dholab_30303_11 dholab_carton_0067 2024-06-17 2024-07-22 qPCR DHO_CN_HPAIspecific01_primers.fasta DHO_CN_HPAIspecific01_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE KY dholab 2024-06-18
16 changes: 8 additions & 8 deletions README.md
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Expand Up @@ -22,16 +22,16 @@ To submit results of your own, read over our [proposal instructions](docs/propos
Processing Plant State | Total Cartons | Positive Cartons | Negative Cartons | Latest Date Sampled
------------------------|-----------------|--------------------|--------------------|---------------------
CA | 1 | 0 | 1 | 2024-05-20
CO | 6 | 5 | 1 | 2024-06-05
CO | 7 | 6 | 1 | 2024-06-18
FL | 1 | 0 | 1 | 2024-05-20
IA | 6 | 0 | 6 | 2024-06-05
IA | 7 | 0 | 7 | 2024-06-18
ID | 1 | 0 | 1 | 2024-05-20
IL | 2 | 0 | 2 | 2024-06-05
IN | 4 | 1 | 3 | 2024-06-05
IL | 3 | 0 | 3 | 2024-06-18
IN | 5 | 1 | 4 | 2024-06-18
KS | 1 | 0 | 1 | 2024-05-20
KY | 2 | 1 | 1 | 2024-05-20
MI | 7 | 4 | 3 | 2024-06-05
MN | 3 | 0 | 3 | 2024-06-05
KY | 3 | 1 | 2 | 2024-06-18
MI | 8 | 5 | 3 | 2024-06-18
MN | 4 | 0 | 4 | 2024-06-18
MO | 1 | 0 | 1 | 2024-05-20
NC | 1 | 0 | 1 | 2024-05-20
NY | 2 | 0 | 2 | 2024-05-20
Expand All @@ -40,7 +40,7 @@ OR | 1 | 0 | 1
TX | 2 | 1 | 1 | 2024-06-05
UT | 1 | 0 | 1 | 2024-05-02
VA | 1 | 0 | 1 | 2024-05-02
WI | 11 | 0 | 1e+01 | 2024-06-05
WI | 15 | 0 | 2e+01 | 2024-06-18

## Sampling Dairy Products for HPAI RNA

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9 changes: 8 additions & 1 deletion scripts/positivity_tally.py
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Expand Up @@ -92,8 +92,15 @@ def main() -> None:
## Sort the results DataFrame alphabetically by state
sorted_results_df = results_df.sort_values(by="Processing Plant State")

# Make all the numbers integers so we don't have to bother with float formatting
int_cols = ["Total Cartons",
"Negative Cartons",
"Positive Cartons",
]
sorted_results_df[int_cols] = sorted_results_df[int_cols].astype(int)

## Save sorted_results_df as a tsv file
sorted_results_df.to_csv(output_path, sep="\t", index=False, float_format="%.01g")
sorted_results_df.to_csv(output_path, sep="\t", index=False)


if __name__ == "__main__":
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