run file

flare/subformula_assign/run.sh

@@ -1,11 +1,15 @@
-# SPEC_FILES="/data/yzhouc01/spectra_data/combined_msgym_nist23_multiplex.tsv"
-# OUTPUT_DIR="/data/yzhouc01/spectra_data/subformulae"
-# MAX_FORMULAE=60
-# LABELS_FILE="/data/yzhouc01/spectra_data/combined_msgym_nist23_multiplex.tsv"
+#!/usr/bin/env bash
+# Assign subformulae with MIST (see README). Set paths via environment variables.
+set -euo pipefail
 
-SPEC_FILES="/data/yzhouc01/cancer/breast_cancer_data.tsv"
-OUTPUT_DIR="/data/yzhouc01/cancer/subformulae"
-MAX_FORMULAE=60
-LABELS_FILE="/data/yzhouc01/cancer/breast_cancer_data.tsv"
+REPO_ROOT="$(cd "$(dirname "$0")/../.." && pwd)"
+SPEC_FILES="${SPEC_FILES:-${REPO_ROOT}/data/sample/data.tsv}"
+OUTPUT_DIR="${OUTPUT_DIR:-${REPO_ROOT}/data/sample/subformulae}"
+LABELS_FILE="${LABELS_FILE:-$SPEC_FILES}"
+MAX_FORMULAE="${MAX_FORMULAE:-60}"
 
-python assign_subformulae.py --spec-files $SPEC_FILES --output-dir $OUTPUT_DIR --max-formulae $MAX_FORMULAE --labels-file $LABELS_FILE 
+python assign_subformulae.py \
+  --spec-files "$SPEC_FILES" \
+  --output-dir "$OUTPUT_DIR" \
+  --max-formulae "$MAX_FORMULAE" \
+  --labels-file "$LABELS_FILE"