Commit 8fbfdb2f authored by Carlos de Lannoy's avatar Carlos de Lannoy
Browse files

update to match revised paper

parent 97cbe912
......@@ -9,46 +9,68 @@ set -euo pipefail
# environment in scripts/env.yml is installed and activated first!
# Analyze simulated data classification
#for f in simulated/data/*; do
# bn=$(basename $f)
# echo "Evaluating traces for ${bn}..."
# python scripts/evaluate_traces.py --fb "simulated/eval/${bn}_fb/" --manual "${f}/dats_labeled" \
# --target-states $(cat "${f}/target_states.txt") \
# --outdir "simulated/eval/${bn}_eval/"
# echo "Done"
#done
#
#echo "evaluating traces for 5_10_state_equidist_fb..."
#python scripts/evaluate_traces.py --fb "simulated/eval_supplementary/5_10_state_equidist_fb/" \
# --manual "simulated/data/4_10_state_equidist/dats_labeled/" \
# --target-states 1 2 3 4 5 6 7 8 9 10 11 \
# --outdir "simulated/eval_supplementary/5_10_state_equidist_eval/"
#echo "Done"
# Generate fig. 3
for f in simulated/data/*; do
bn=$(basename $f)
echo "Evaluating traces for ${bn}..."
python scripts/evaluate_traces.py --fb "simulated/eval/${bn}_fb/" --manual "${f}/dats_labeled" \
--target-states $(cat "${f}/target_states.txt") \
--outdir "simulated/eval/${bn}_eval/"
echo "Done"
done
echo "evaluating traces for 5_10_state_equidist_fb..."
python scripts/evaluate_traces.py --fb "simulated/eval_supplementary/5_10_state_equidist_fb/" \
--manual "simulated/data/4_10_state_equidist/dats_labeled/" \
--target-states 1 2 3 4 5 6 7 8 9 10 11 \
--outdir "simulated/eval_supplementary/5_10_state_equidist_eval/"
echo "Done"
## Generate fig. 3
python scripts/generate_sim_fig.py --eval-dirs simulated/eval/*_eval --cat-names 1_2_state_don_eval 2_3_state_don 3_3_state_kinetic 4_10_state_equidist --out-svg "simulated/eval/sim_figure.svg"
# Generate supplementary figure S3
python scripts/generate_sim_fig.py --eval-dirs simulated/eval_supplementary/*_eval --cat-names 5_10_state_equidist --out-svg "simulated/eval_supplementary/sim_10_state_equidist_vanilla.svg"
python scripts/generate_sim_fig.py --eval-dirs simulated/eval_supplementary/*_eval --cat-names 5_10_state_equidist --out-svg "simulated/eval_supplementary/sim_10_state_equidist_vanilla.svg"
# Analyze in vitro data classification
for f in in_vitro/data/*; do
bn=$(basename $f)
echo "Evaluating traces for ${bn} , generate element of figure S5..."
python scripts/evaluate_traces.py --fb "in_vitro/eval/${bn}_fb/" --manual "${f}/dats_labeled" \
--target-states $(cat "${f}/target_states.txt") \
--outdir "in_vitro/eval/${bn}_eval/"
echo "Done"
done
echo "Evaluating data for in vitro supplementary..."
for f in in_vitro/data/*; do
bn=$(basename $f)
echo "Evaluating traces for ${bn}..."
python scripts/evaluate_traces.py --fb "in_vitro/eval_supplementary/${bn}_fb/" --manual "${f}/dats_labeled" \
--target-states $(cat "${f}/target_states.txt") \
--outdir "in_vitro/eval_supplementary/${bn}_eval/"
echo "Done"
done
# Generate figure 4
python scripts/generate_invitro_fig.py --eval-dirs in_vitro/eval/*_eval --cat-names 1_2_state_donor_immobilized 2_2_state_acceptor_immobilized 3_tandem_10nt 4_kinetic_fingerprint --out-svg "in_vitro/eval/in_vitro_fig.svg" --example-traces "in_vitro/eval/example_traces.tsv"
echo "Generating figure 4"
python scripts/generate_invitro_fig.py \
--eval-dirs in_vitro/eval/*_eval \
--cat-names 1_2_state_donor_immobilized 2_2_state_acceptor_immobilized 3_tandem_10nt 4_kinetic_fingerprint \
--out-svg "in_vitro/eval/in_vitro_fig.svg" --example-traces "in_vitro/eval/example_traces.tsv"
echo "Done"
# Generate supplementary figure S4
python scripts/generate_invitro_fig.py --eval-dirs in_vitro/eval_supplementary/*_eval --cat-names 1_2_state_donor 2_2_state_acceptor 3_tandem_10nt 4_kinetic_fingerprint --out-svg "in_vitro/eval_supplementary/in_vitro_fig_supplementary.svg"
echo "Generating supp figure S4"
python scripts/generate_invitro_fig.py \
--eval-dirs in_vitro/eval_supplementary/*_eval \
--cat-names 1_2_state_donor 2_2_state_acceptor 3_tandem_10nt 4_kinetic_fingerprint \
--out-svg "in_vitro/eval_supplementary/in_vitro_fig_supplementary.svg"
echo "Done"
# Generate supplementary figure S6
echo "Generating supp figure S6"
python scripts/compare_other_tools.py --eval-dir in_vitro/eval \
--experiments 1_2_state_donor_immobilized 2_2_state_acceptor_immobilized 3_tandem_10nt 4_kinetic_fingerprint \
--data-dir in_vitro/data \
--out-dir in_vitro/tool_comparison
echo "Done"
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