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Create test.htmll

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tpollina 2019-12-01 18:35:02 -08:00 committed by GitHub
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commit de835351cf
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cat "/media/tpollina/ACQUISITION/PlanktonScope_V2/exp_new_03/"$folder"/OBJECTS/ecotaxa_size_mesurement.tsv" | head -n 1 > /home/tpollina/Desktop/day_night_pyro/table.tsv
for folder in 0 1 10 11 14 15 17 18 2 20 21 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 6 7 9
do
cat "/media/tpollina/ACQUISITION/PlanktonScope_V2/exp_new_03/"$folder"/OBJECTS/ecotaxa_size_mesurement.tsv" | tail -n +3 >> /home/tpollina/Desktop/day_night_pyro/table.tsv
cp /media/tpollina/ACQUISITION/PlanktonScope_V2/exp_new_03/$folder/OBJECTS/*.jpg /home/tpollina/Desktop/day_night_pyro/
done
cat /home/tpollina/Desktop/day_night_pyro/table.tsv | head -n 1 > /home/tpollina/Desktop/day_night_pyro/simplified.tsv
#!/bin/bash
for i in $( ls *.jpg); do
grep $i table.tsv >> /home/tpollina/Desktop/day_night_pyro/simplified.tsv
done
cat "/media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/Chile_EXPORT/CHILE_DAY2_ST4_D9_2/ecotaxa_size_mesurement.tsv" | head -n 1 > /media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/figure_5_analysis_chile.tsv
for replicat in 1 2
do
for depth in 0 1 2 3 4 5 6 7 8 9 10
do
cat "/media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/Chile_EXPORT/CHILE_DAY2_ST4_D"$depth"_"$replicat"/ecotaxa_size_mesurement.tsv" | tail -n +3 >> /media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/figure_5_analysis_chile.tsv
done
done
for replicat in 1 2
do
for depth in 0 1 2 3 4 5 6 7 8 9 10
do
echo $depth
cat "/media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/Chile_EXPORT/CHILE_DAY2_ST4_D"$depth"_"$replicat"/ecotaxa_size_mesurement.tsv" | tail -n +3 | awk '{ total += $41; count++ } END { print total/count }' >> /media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/mean_eccentricity.tsv
done
done
for replicat in 1 2; do
for depth in 0 1 2 3 4 5 6 7 8 9 10; do
echo $depth
cp "/media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/Chile_EXPORT/CHILE_DAY2_ST4_D"$depth"_"$replicat"/"
done
done
for depth in 0 1 2 3 4 5 6 7 8 9 10; do
for obj in $(cat table.csv | grep $depth | awk -F ',' '{print $2}'); do
cp "/media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/Chile_EXPORT/CHILE_DAY2_ST4_D"$depth"_"0"/"$obj .
cp "/media/tpollina/TPOLLINA_WORK1/PLANKTOSCOPE/ACQUISITION/ENVIRONNEMENTAL_SAMPLES/CHILE/Chile_EXPORT/CHILE_DAY2_ST4_D"$depth"_"1"/"$obj .
done
done
for replicat in 1 2; do
for depth in 0 1 2 3 4 5 6 7 8 9 10; do
echo "cp CHILE_DAY2_ST4_D"$depth"_"$replicat"/*.jpg" ALL_OBJECTS/
done
done