update shell scripts

deploy_regression_crossval.sh

@@ -1,13 +1,15 @@
-full_dir=/home/omarelnahhas/omars_hdd/HRD/CPTAC-FEATURES_test/CPTAC_UCEC_features
-dir=${full_dir##*/}
-target=LOH
-for fold in 0_020r2 1_021r2 2_032r2 3_020r2 4_010r2
+full_dir=/home/omarelnahhas/omars_hdd/omar/immunoproject_project/top5_regression_binarybalanced/*
+for dir in /home/omarelnahhas/omars_hdd/omar/immunoproject_project/top5_regression_binarybalanced/*
+do
+target=${dirs##*/}
+for fold in 0 1 2 3 4
 do
 	python -m marugoto.mil deploy \
-		--clini-table /home/omarelnahhas/HRD_project/CPTAC_CLINIC.xlsx \
-		--slide-csv /home/omarelnahhas/omars_hdd/HRD/CPTAC-FEATURES_test/${dir}/*.csv \
-		--feature-dir /home/omarelnahhas/omars_hdd/HRD/CPTAC-FEATURES_test/${dir}/xiyue-wang \
-		--output-path /home/omarelnahhas/HRD_project/${target}/deploy_${dir}_DIR/fold-${fold} \
-		--target-label "${target}" \
-		--model-path /home/omarelnahhas/HRD_project/${target}/TCGA-UCEC-DX-features_DIR/fold-${fold}/*.pkl
+		--clini-table /home/omarelnahhas/omars_hdd/omar/FOCUS/FOCUS1_CLINI.xlsx \
+		--slide-csv /home/omarelnahhas/omars_hdd/omar/FOCUS/*_SLIDE.csv \
+		--feature-dir /home/omarelnahhas/omars_hdd/omar/FOCUS/Xiyue-Wang_v2 \
+		--output-path ${dir}/deploy_${target}_FOCUS_CRC/fold-${fold} \
+		--target-label "dummy" \
+		--model-path "${dir}"/TCGA-CRC-DX-features/fold-${fold}/*.pkl
+done
 done

regression_crossval.sh

@@ -1,11 +1,11 @@
-full_dir=/home/omarelnahhas/omars_hdd/HRD/TCGA-FEATURES_train/TCGA-UCEC-DX-features
-dir=${full_dir##*/}
-for target in CX8 CX9 CX10 CX11 CX12 CX13 CX14 CX15 CX16 CX17
+for full_dir in /home/omarelnahhas/omars_hdd/omar/immunoproject/*
 do
+	dir=${full_dir##*/}
+	echo "Running Fraction Genome Altered for ${dir}"
 	python -m marugoto.mil crossval \
-		--clini-excel /home/omarelnahhas/TCGA_Markowetz/norm_CLINI_Markowetz.csv \
-		--slide-csv /home/omarelnahhas/TCGA_Markowetz/tcga_merkowetz_SLIDE.csv  \
-		--feature-dir /mnt/Sirius_03_empty/TCGA-ALL-FEATURES/ \
-		--output-path /home/omarelnahhas/TCGA_Markowetz/${target}/ALL_FEATS_DIR \
-		--target-label "${target}"
+		--clini-excel /home/omarelnahhas/omars_hdd/omar/immunoproject_project/clini_positive_control/Fraction_GA.xlsx \
+		--slide-csv ${full_dir}/*_SLIDE.csv  \
+		--feature-dir ${full_dir}/xiyue-wang-macenko \
+		--output-path /home/omarelnahhas/omars_hdd/omar/immunoproject_project/clini_positive_control/experiments/Fraction_GA/${dir} \
+		--target-label Fraction_GA
 done