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1914 lines (1646 loc) · 84 KB
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## Go to GISAID and go to the Search tab
## Set location to "District of Columbia"
## Select all viral sequences and download "Input for Augur Pipeline"
## Rename the metadata file in the format: gisaid*.tsv
## Make a copy of the .tsv file. In one file, delete column E "date". This will be the file you use for submission date.
## In the other file, delete column AA "date_submitted". This will be the file you use for collection date.
## Be sure to run the script in the same directory as only ONE .tsv file at a time.
## Go to GISAID and go to the Search tab
## Set location to "District of Columbia"
## Select all viral sequences and download "Input for Augur Pipeline"
## Rename the metadata file in the format: gisaid*.tsv
## Make a copy of the .tsv file. In one file, delete column E "date". This will be the file you use for submission date.
## In the other file, delete column AA "date_submitted". This will be the file you use for collection date.
## Be sure to run the script in the same directory as only ONE .tsv file at a time.
#### JANUARY 2020
grep "2020-01" gisaid*.tsv > input_by_month.tsv
echo "JANUARY 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### FEBRUARY 2020
grep "2020-02" gisaid*.tsv > input_by_month.tsv
echo "FEBRUARY 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### MARCH 2020
grep "2020-03" gisaid*.tsv > input_by_month.tsv
echo "MARCH 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### APRIL 2020
grep "2020-04" gisaid*.tsv > input_by_month.tsv
echo "APRIL 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### MAY 2020
grep "2020-05" gisaid*.tsv > input_by_month.tsv
echo "MAY 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### JUNE 2020
grep "2020-06" gisaid*.tsv > input_by_month.tsv
echo "JUNE 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### JULY 2020
grep "2020-07" gisaid*.tsv > input_by_month.tsv
echo "JULY 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### AUGUST 2020
grep "2020-08" gisaid*.tsv > input_by_month.tsv
echo "AUGUST 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### SEPTEMBER 2020
grep "2020-09" gisaid*.tsv > input_by_month.tsv
echo "SEPTEMBER 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### OCTOBER 2020
grep "2020-10" gisaid*.tsv > input_by_month.tsv
echo "OCTOBER 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### NOVEMBER 2020
grep "2020-11" gisaid*.tsv > input_by_month.tsv
echo "NOVEMBER 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### DECEMBER 2020
grep "2020-12" gisaid*.tsv > input_by_month.tsv
echo "DECEMBER 2020"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)
VOC3=$(grep -cw "B.1.351" DC_all_variants.tsv)
VOC4=$(grep -cw "B.1.617.2" DC_all_variants.tsv)
echo "Variants of Interest/Concern in DC"
printf "B.1.427\t%s\t%s\n" "${VOI1}"
printf "B.1.429\t%s\t%s\n" "${VOI2}"
printf "B.1.525\t%s\t%s\n" "${VOI3}"
printf "B.1.526\t%s\t%s\n" "${VOI4}"
printf "B.1.617.1\t%s\t%s\n" "${VOI5}"
printf "B.1.617.3\t%s\t%s\n" "${VOI6}"
printf "P.2\t%s\t%s\n" "${VOI7}"
printf "B.1.1.7\t%s\t%s\n" "${VOC1}"
printf "P.1\t%s\t%s\n" "${VOC2}"
printf "B.1.351\t%s\t%s\n" "${VOC3}"
printf "B.1.617.2\t%s\t%s\n" "${VOC4}"
tail +2 DC_all_variants.tsv | cut -f 1-27 | grep -w "DC-DFS-PHL" | sort | uniq > DC_PHL.tsv
DFSVOI1=$(grep -cw "B.1.427" DC_PHL.tsv)
DFSVOI2=$(grep -cw "B.1.429" DC_PHL.tsv)
DFSVOI3=$(grep -cw "B.1.525" DC_PHL.tsv)
DFSVOI4=$(grep -cw "B.1.526" DC_PHL.tsv)
DFSVOI5=$(grep -cw "B.1.617.1" DC_PHL.tsv)
DFSVOI6=$(grep -cw "B.1.617.3" DC_PHL.tsv)
DFSVOI7=$(grep -cw "P.2" DC_PHL.tsv)
DFSVOC1=$(grep -cw "B.1.1.7" DC_PHL.tsv)
DFSVOC2=$(grep -cw "P.1" DC_PHL.tsv)
DFSVOC3=$(grep -cw "B.1.351" DC_PHL.tsv)
DFSVOC4=$(grep -cw "B.1.617.2" DC_PHL.tsv)
echo "Variants of Interest/Concern sequenced by PHL"
printf "B.1.427\t%s\t%s\n" "${DFSVOI1}"
printf "B.1.429\t%s\t%s\n" "${DFSVOI2}"
printf "B.1.525\t%s\t%s\n" "${DFSVOI3}"
printf "B.1.526\t%s\t%s\n" "${DFSVOI4}"
printf "B.1.617.1\t%s\t%s\n" "${DFSVOI5}"
printf "B.1.617.3\t%s\t%s\n" "${DFSVOI6}"
printf "P.2\t%s\t%s\n" "${DFSVOI7}"
printf "B.1.1.7\t%s\t%s\n" "${DFSVOC1}"
printf "P.1\t%s\t%s\n" "${DFSVOC2}"
printf "B.1.351\t%s\t%s\n" "${DFSVOC3}"
printf "B.1.617.2\t%s\t%s\n" "${DFSVOC4}"
rm DC_all_variants.tsv DC_B117.tsv DC_B1351.tsv DC_B1427.tsv DC_B1429.tsv DC_B1525.tsv DC_B1526.tsv DC_B16171.tsv DC_B16172.tsv DC_B16173.tsv DC_P1.tsv DC_P2.tsv DC_PHL.tsv
rm input_by_month.tsv
#### JANUARY 2021
grep "2021-01" gisaid*.tsv > input_by_month.tsv
echo "JANUARY 2021"
(printf '%s: ' "Total SARS-CoV-2 in DC" ; grep -c "hCoV-19" input_by_month.tsv)
(printf '%s: ' "SARS-CoV-2 sequenced by DFS" ; grep -c "DC-DFS-PHL" input_by_month.tsv)
## looking for variants of interest
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.427" | sort | uniq > DC_B1427.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.429" | sort | uniq > DC_B1429.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.525" | sort | uniq > DC_B1525.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.526" | sort | uniq > DC_B1526.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.1" | sort | uniq > DC_B16171.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.3" | sort | uniq > DC_B16173.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.2" | sort | uniq > DC_P2.tsv
## looking for variants of concern
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.1.7" | sort | uniq > DC_B117.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "P.1" | sort | uniq > DC_P1.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.351" | sort | uniq > DC_B1351.tsv
tail +2 input_by_month.tsv | cut -f 1-27 | grep -w "B.1.617.2" | sort | uniq > DC_B16172.tsv
cat DC*.tsv > DC_all_variants.tsv
VOI1=$(grep -cw "B.1.427" DC_all_variants.tsv)
VOI2=$(grep -cw "B.1.429" DC_all_variants.tsv)
VOI3=$(grep -cw "B.1.525" DC_all_variants.tsv)
VOI4=$(grep -cw "B.1.526" DC_all_variants.tsv)
VOI5=$(grep -cw "B.1.617.1" DC_all_variants.tsv)
VOI6=$(grep -cw "B.1.617.3" DC_all_variants.tsv)
VOI7=$(grep -cw "P.2" DC_all_variants.tsv)
VOC1=$(grep -cw "B.1.1.7" DC_all_variants.tsv)
VOC2=$(grep -cw "P.1" DC_all_variants.tsv)