tools_playground

1. Extract basic metrics from ROIs

extract_roiset_metrics_to_csv.py \
    -i /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230504_1510_S0096_0001/raws/ \
    -r /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230504_1510_S0096_0001/Analysis/S0096_RoiSet.zip \
    -o S0096.csv

extract_roiset_metrics_to_csv.py \
    -i /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230504_1540_S0097_0001/raws/ \
    -r /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230504_1540_S0097_0001/Analysis/S0097_RoiSet.zip \
    -o S0097.csv

extract_roiset_metrics_to_csv.py \
    -i /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230504_1607_S0098_0001/raws/ \
    -r /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230504_1607_S0098_0001/Analysis/S0098_RoiSet.zip \
    -o S0098.csv

extract_roiset_metrics_to_csv.py \
    -i /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230504_1631_S0099_0001/raws/ \
    -r /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230504_1631_S0099_0001/Analysis/S0099_RoiSet5.zip \
    -o S0099.csv

plot_roiset_run_comparison.py -h

plot_roiset_run_comparison.py -i S0096.csv S0097.csv S0098.csv S0099.csv -o orig.jpg

plot_roiset_run_comparison.py -i S0096.csv S0097.csv S0098.csv S0099.csv -o normalized.jpg -n

Create browser based graph with spot trajectories

plot_spot_trajectories.py -i analysis/metrics.csv 
plot_spot_trajectories.py -i analysis/metrics.csv -c G445 G525 R590 B445
plot_spot_trajectories.py -i analysis/metrics.csv -s S1 S2 -c G445 G525 R590 B445
plot_spot_trajectories.py -i analysis/metrics.csv -o analysis/trajectories.png

2. Create triangle graphs

extract_roiset_pixel_data.py -i . -r RoiSet.zip -o RoiSet.csv -e 7 -n 500

triangle_graph.py -i RoiSet.csv -o triangle.png -g -m 20 33.3 12

triangle_graph.py -i RoiSet.csv -o triangle.png -g -c G445 G525 R590 B445

triangle_graph.py -i RoiSet.csv -o triangle.png -g -s A C G T BG S1 S2

triangle_graph.py -i RoiSet.csv -o triangle.png -g -c G445 G525 R590 B445 -s A C G T BG S1 S2

3. Create basic basecaller graph

extract_roiset_pixel_data.py -e 7 -n 500 \
    -i /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230517_1458_S0115_0001/raws \
    -r /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230517_1458_S0115_0001/analysis/RoiSetJRC4_28spotsACGT.zip \
    -o /tmp/roi_pixel_data.csv
    
color_transformation.py \
    -i /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230517_1458_S0115_0001/raws \
    -r /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230517_1458_S0115_0001/analysis/RoiSetJRC4_28spotsACGT.zip \
    -p /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230517_1458_S0115_0001/analysis/roi_pixel_data.csv \
    -o /tmp



cd /mnt/nas_share/GoogleData/InstrumentData/MK27_02/20230517_1458_S0115_0001

extract_roiset_pixel_data.py \
    -e 7 \
    -n 500 \
    -i raws \
    -r analysis/RoiSetJRC4_28spotsACGT.zip \
    -o /tmp/spot_pixel_data.csv

color_transformation.py \
    -i raws \
    -r analysis/RoiSetJRC4_28spotsACGT.zip \
    -p analysis/spot_pixel_data.csv \
    -c G445 G525 R590 B445 \
    -s A C G T BG S1 S2 \
    -o /tmp