seq_emb.sh

Author: tanchengzi0430

scripts/RNAERNIE/seq_emb.sh

@@ -1,20 +1,17 @@
 #!/bin/bash
 
-export model_location="/home/ma_run_ze/lzm/rnagym/fitness/baselines/RNA_FM/RNA-FM"
-export reference_sheet="/home/ma_run_ze/lzm/rnagym/fitness/reference_sheet_final.csv"
-export output_dir="/data_share/marunze/lzm/rnagym/fitness/embeddings/RNAernie/"
-export dms_data_dir="/home/ma_run_ze/lzm/rnagym/fitness/fitness_processed_assays"
+
+export model_location=""
+export reference_sheet=""
+export output_dir=""
+export dms_data_dir=""
 conda activate rnaernie
 export model_checkpoint="src/"
 export vocab_path="src/vocab_1MER.txt"
 mkdir -p "$output_dir"
-export HF_ENDPOINT=https://hf-mirror.com
-export CUDA_VISIBLE_DEVICES=4  # Set to the GPU you want to use
-# Get the current index from the array (0-31)
-    # Run the scoring script with the array task ID
     python3 seq_emb.py \
     --output_dir_path "$output_dir" \
     --ref_sheet "$reference_sheet" \
     --dms_dir_path "$dms_data_dir" \
     --model_checkpoint "$model_checkpoint" \
-    --vocab_path "$vocab_path" 
+    --vocab_path "$vocab_path"