Simplify data_evaluation - no more monoallelic

downloads-generation/data_evaluation/GENERATE.sh

@@ -55,29 +55,29 @@ else
 fi
 
 ### GENERATE BENCHMARK: MONOALLELIC
-for kind in train_excluded all
-do
-    EXCLUDE_TRAIN_DATA=""
-    if [ "$kind" == "train_excluded" ]
-    then
-        EXCLUDE_TRAIN_DATA="$(mhcflurry-downloads path models_class1_pan_variants)/models.no_additional_ms/train_data.csv.bz2"
-    fi
-
-    if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.monoallelic.$kind.csv.bz2" ]
-    then
-        echo "Reusing existing monoallelic benchmark: benchmark.monoallelic.$kind.csv.bz2"
-    else
-        cp $SCRIPT_DIR/make_benchmark.py .
-        time python make_benchmark.py \
-            --hits "$(pwd)/hits_with_tpm.csv.bz2" \
-            --proteome-peptides "$(mhcflurry-downloads path data_predictions)/proteome_peptides.all.csv.bz2" \
-            --decoys-per-hit 110 \
-            --exclude-train-data "$EXCLUDE_TRAIN_DATA" \
-            --only-format MONOALLELIC \
-            --out "$(pwd)/benchmark.monoallelic.$kind.csv"
-        bzip2 -f benchmark.monoallelic.$kind.csv
-    fi
-done
+#for kind in train_excluded all
+#do
+#    EXCLUDE_TRAIN_DATA=""
+#    if [ "$kind" == "train_excluded" ]
+#    then
+#        EXCLUDE_TRAIN_DATA="$(mhcflurry-downloads path models_class1_pan_variants)/models.no_additional_ms/train_data.csv.bz2"
+#    fi
+#
+#    if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.monoallelic.$kind.csv.bz2" ]
+#    then
+#        echo "Reusing existing monoallelic benchmark: benchmark.monoallelic.$kind.csv.bz2"
+#    else
+#        cp $SCRIPT_DIR/make_benchmark.py .
+#        time python make_benchmark.py \
+#            --hits "$(pwd)/hits_with_tpm.csv.bz2" \
+#            --proteome-peptides "$(mhcflurry-downloads path data_predictions)/proteome_peptides.all.csv.bz2" \
+#            --decoys-per-hit 110 \
+#            --exclude-train-data "$EXCLUDE_TRAIN_DATA" \
+#            --only-format MONOALLELIC \
+#            --out "$(pwd)/benchmark.monoallelic.$kind.csv"
+#        bzip2 -f benchmark.monoallelic.$kind.csv
+#    fi
+#done
 
 ### GENERATE BENCHMARK: MULTIALLELIC
 for kind in train_excluded all
@@ -110,21 +110,21 @@ mkdir commands
 for kind in train_excluded all
 do
     ### AFFINITY PREDICTOR VARIANT: MONOALLELIC
-    if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.monoallelic.no_additional_ms.$kind.csv.bz2" ]
-    then
-        echo "Reusing existing monoallelic benchmark predictions"
-    else
-        echo time mhcflurry-predict \
-            "$(pwd)/benchmark.monoallelic.$kind.csv.bz2" \
-            --allele-column hla \
-            --prediction-column-prefix no_additional_ms_ \
-            --models \""$(mhcflurry-downloads path models_class1_pan_variants)/models.no_additional_ms"\" \
-            --affinity-only \
-            --no-affinity-percentile \
-            --out "$(pwd)/benchmark.monoallelic.no_additional_ms.$kind.csv" \
-            --no-throw >> commands/monoallelic.$kind.sh
-        echo bzip2 -f "$(pwd)/benchmark.monoallelic.no_additional_ms.$kind.csv" >> commands/monoallelic.$kind.sh
-    fi
+    #if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.monoallelic.no_additional_ms.$kind.csv.bz2" ]
+    #then
+    #    echo "Reusing existing monoallelic benchmark predictions"
+    #else
+    #    echo time mhcflurry-predict \
+    #        "$(pwd)/benchmark.monoallelic.$kind.csv.bz2" \
+    #        --allele-column hla \
+    #        --prediction-column-prefix no_additional_ms_ \
+    #        --models \""$(mhcflurry-downloads path models_class1_pan_variants)/models.no_additional_ms"\" \
+    #        --affinity-only \
+    #        --no-affinity-percentile \
+    #        --out "$(pwd)/benchmark.monoallelic.no_additional_ms.$kind.csv" \
+    #        --no-throw >> commands/monoallelic.$kind.sh
+    #    echo bzip2 -f "$(pwd)/benchmark.monoallelic.no_additional_ms.$kind.csv" >> commands/monoallelic.$kind.sh
+    #fi
 
 
     ### AFFINITY PREDICTORS: MULTIALLELIC
@@ -143,7 +143,8 @@ do
         echo bzip2 -f "$(pwd)/benchmark.multiallelic.production.$kind.csv" >> commands/multiallelic.production.$kind.sh
     fi
 
-    for variant in no_additional_ms compact_peptide affinity_only no_pretrain single_hidden_no_pretrain 500nm
+    #for variant in no_additional_ms compact_peptide affinity_only no_pretrain single_hidden_no_pretrain 500nm
+    for variant in 50nm
     do
         if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.multiallelic.${variant}.$kind.csv.bz2" ]
         then
@@ -195,17 +196,17 @@ do
     ### PRECOMPUTED ####
     for variant in netmhcpan4.ba netmhcpan4.el mixmhcpred
     do
-        if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.monoallelic.${variant}.$kind.csv.bz2" ]
-        then
-            echo "Reusing existing monoallelic ${variant}"
-        else
-            cp $SCRIPT_DIR/join_with_precomputed.py .
-            echo time python join_with_precomputed.py \
-                \""$(pwd)/benchmark.monoallelic.$kind.csv.bz2"\" \
-                ${variant} \
-                --out "$(pwd)/benchmark.monoallelic.${variant}.$kind.csv" >> commands/monoallelic.${variant}.$kind.sh
-            echo bzip2 -f "$(pwd)/benchmark.monoallelic.${variant}.$kind.csv"  >> commands/monoallelic.${variant}.$kind.sh
-        fi
+        #if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.monoallelic.${variant}.$kind.csv.bz2" ]
+        #then
+        #    echo "Reusing existing monoallelic ${variant}"
+        #else
+        #    cp $SCRIPT_DIR/join_with_precomputed.py .
+        #    echo time python join_with_precomputed.py \
+        #        \""$(pwd)/benchmark.monoallelic.$kind.csv.bz2"\" \
+        #        ${variant} \
+        #        --out "$(pwd)/benchmark.monoallelic.${variant}.$kind.csv" >> commands/monoallelic.${variant}.$kind.sh
+        #    echo bzip2 -f "$(pwd)/benchmark.monoallelic.${variant}.$kind.csv"  >> commands/monoallelic.${variant}.$kind.sh
+        #fi
 
         if [ "$2" == "continue-incomplete" ] && [ -f "benchmark.multiallelic.${variant}.$kind.csv.bz2" ]
         then