added unzipping functionality for mimic iv example

mmcdermott · Jul 10, 2024 · 2723b3e · 2723b3e
1 parent c96c948
commit 2723b3e
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/MIMIC-IV_Example/joint_script.sh b/MIMIC-IV_Example/joint_script.sh
@@ -42,6 +42,9 @@ shift 4
 echo "Running pre-MEDS conversion."
 ./MIMIC-IV_Example/pre_MEDS.py raw_cohort_dir="$MIMICIV_RAW_DIR" output_dir="$MIMICIV_PREMEDS_DIR"
 
+echo "Unzipping the pre-MEDS gunzip csv files."
+for file in ${MIMICIV_PREMEDS_DIR}/*/*.csv.gz; do gzip -d --force "$file"; done
+
 echo "Running shard_events.py with $N_PARALLEL_WORKERS workers in parallel"
 ./scripts/extraction/shard_events.py \
     --multirun \