fix

downloads-generation/models_class1_pan/GENERATE.sh

@@ -54,11 +54,15 @@ do
         --num-jobs 0 \
         --num-jobs $NUM_JOBS --max-tasks-per-worker 1 --gpus $GPUS --max-workers-per-gpu 1
 
+    # For now we calibrate percentile ranks only for alleles for which there
+    # is training data. Calibrating all alleles would be too slow.
+    # This could be improved though.
     time mhcflurry-calibrate-percentile-ranks \
         --models-dir models.${kind} \
         --match-amino-acid-distribution-data "$MODELS_DIR/train_data.csv.bz2" \
         --motif-summary \
         --num-peptides-per-length 100000 \
+        --allele $(bzcat "$MODELS_DIR/train_data.csv.bz2" | cut -f 1 -d , | grep -v allele | uniq | sort | uniq) \
         --verbosity 1 \
         --num-jobs $NUM_JOBS --max-tasks-per-worker 1 --gpus $GPUS --max-workers-per-gpu 1
 done