Add a wrapper script for command-line predictions

README.md

@@ -51,6 +51,15 @@ conda activate rarefold
 bash predict.sh
 ```
 
+## Running Custom Predictions
+For running new predictions with your own data, a wrapper script `run_rarefold_predict.sh` is provided which accepts command-line arguments.
+
+To see all available options and their defaults, run:
+```bash
+conda activate rarefold
+./run_rarefold_predict.sh --help
+```
+
 
 # Design using EvoBindRare
 ## Design linear or cyclic peptide binders incorporating noncanonical amino acids

run_rarefold_predict.sh

@@ -0,0 +1,210 @@
+#!/usr/bin/env bash
+
+################################################################################
+# TJN25 Contributed Header
+#
+# This section adds robust command-line argument parsing and path handling
+# to make the script a reusable tool.
+################################################################################
+
+# Set BASE as the install directory of the script
+SOURCE=${BASH_SOURCE[0]}
+while [ -L "$SOURCE" ]; do
+  DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+  SOURCE=$(readlink "$SOURCE")
+  [[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE
+done
+BASE=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
+
+# Set some default values
+NUM_REC_DEFAULT=3
+OUTDIR_DEFAULT="./output"
+PARAMS_DEFAULT="$BASE/data/params/params20000.npy"
+
+
+usage() {
+  cat <<EOF
+Usage: $(basename "$0") -i <ID> [OPTIONS]
+
+Runs the RareFold prediction workflow with robust path handling.
+
+Required Arguments:
+  -i, --id <string>         A unique identifier for this prediction run.
+
+Optional Arguments:
+  -d, --datadir <path>      Directory containing the input FASTA file.
+                            (Default: current directory)
+  -o, --outdir <path>       Directory where all output will be saved.
+                            (Default: ${OUTDIR_DEFAULT})
+  -n, --num-recycles <int>  Number of recycles for the model.
+                            (Default: ${NUM_REC_DEFAULT})
+  -p, --params <file>       Path to the model parameters (.npy) file.
+                            (Default: auto-detected within script directory)
+  --fasta <file>            Override the path to the input FASTA file. By default,
+                            it is assumed to be located at <datadir>/<id>.fasta.
+  --msa <file>              Provide a pre-computed MSA file (.a3m). This will
+                            skip the hhblits execution step.
+  --hhblitsdb <path>        Override the path to the HHblits database.
+                            (Default: auto-detected within script directory)
+  -h, --help                Display this help message and exit.
+
+EOF
+  exit 1
+}
+
+# Variables set by CLI args
+# Required:
+ID=""
+# Optional with defaults:
+DATADIR="."
+NUM_REC=$NUM_REC_DEFAULT
+PARAMS=$PARAMS_DEFAULT
+OUTDIR=$OUTDIR_DEFAULT
+# Optional overrides for constructed paths:
+FASTA_OVERRIDE=""
+MSA_OVERRIDE=""
+HHBLITSDB_OVERRIDE=""
+
+# Get command line args
+while [ $# -gt 0 ]; do
+  case "$1" in
+    -i|--id)
+      if [ -z "$2" ] || [[ "$2" == -* ]]; then echo "Error: $1 requires a value." >&2; exit 1; fi
+      ID="$2"
+      shift 2
+      ;;
+    -d|--datadir)
+      if [ -z "$2" ] || [[ "$2" == -* ]]; then echo "Error: $1 requires a value." >&2; exit 1; fi
+      DATADIR="$2"
+      shift 2
+      ;;
+    -n|--num-recycles)
+      if [ -z "$2" ] || [[ "$2" == -* ]]; then echo "Error: $1 requires a value." >&2; exit 1; fi
+      NUM_REC="$2"
+      shift 2
+      ;;
+    -p|--params)
+      if [ -z "$2" ] || [[ "$2" == -* ]]; then echo "Error: $1 requires a value." >&2; exit 1; fi
+      PARAMS="$2"
+      shift 2
+      ;;
+    -o|--outdir)
+      if [ -z "$2" ] || [[ "$2" == -* ]]; then echo "Error: $1 requires a value." >&2; exit 1; fi
+      OUTDIR="$2"
+      shift 2
+      ;;
+    --fasta)
+      if [ -z "$2" ] || [[ "$2" == -* ]]; then echo "Error: $1 requires a value." >&2; exit 1; fi
+      FASTA_OVERRIDE="$2"
+      shift 2
+      ;;
+    --msa)
+      if [ -z "$2" ] || [[ "$2" == -* ]]; then echo "Error: $1 requires a value." >&2; exit 1; fi
+      MSA_OVERRIDE="$2"
+      shift 2
+      ;;
+    --hhblitsdb)
+      if [ -z "$2" ] || [[ "$2" == -* ]]; then echo "Error: $1 requires a value." >&2; exit 1; fi
+      HHBLITSDB_OVERRIDE="$2"
+      shift 2
+      ;;
+    -h|--help)
+      usage
+      ;;
+    *)
+      echo "Error: Unknown argument: $1" >&2
+      usage
+      ;;
+  esac
+done
+
+
+# Validate required arguments
+if [ -z "$ID" ]; then
+  echo "Error: Missing required argument: -i/--id" >&2
+fi
+
+# Set up remaining variables
+mkdir -p "$OUTDIR"
+
+if [ -n "$FASTA_OVERRIDE" ]; then
+  FASTAFILE="$FASTA_OVERRIDE"
+else
+  FASTAFILE="$DATADIR/$ID.fasta"
+fi
+
+if [ -n "$MSA_OVERRIDE" ]; then
+  MSA_A3M="$MSA_OVERRIDE"
+else
+  MSA_A3M="$OUTDIR/$ID.a3m"
+fi
+
+if [ -n "$HHBLITSDB_OVERRIDE" ]; then
+  HHBLITSDB="$HHBLITSDB_OVERRIDE"
+else
+  HHBLITSDB="$BASE/data/uniclust30_2018_08/uniclust30_2018_08"
+fi
+
+# Ensure the final input FASTA file exists before proceeding
+if [ ! -f "$FASTAFILE" ]; then
+    echo "Error: Input FASTA file not found at: $FASTAFILE" >&2
+    exit 1
+fi
+
+# Construct paths for intermediate and output files
+# The sequence has to be defined with the noncanonical amino acids (NCAAs) in
+# threeletter code separated by hyphens, and the regular in oneletter e.g.
+# >1FU0_A
+# MEKKEFHIVAETGIHARPATLLVQTASKFNSDINLEYKGKSVNLK-SEP-IMGVMSLGVGQGSDVTITVDGADEAEGMAAIVETLQKEGLA
+#
+# We also need a fasta where the NCAA is "X" for the MSA search
+# >1FU0_A
+# MEKKEFHIVAETGIHARPATLLVQTASKFNSDINLEYKGKSVNLKXIMGVMSLGVGQGSDVTITVDGADEAEGMAAIVETLQKEGLA
+FASTAWITHX="$OUTDIR/${ID}_X.fasta"
+
+MSA_FEATS="$OUTDIR/msa_features.pkl"
+
+# Set the hhblits command. Check if hhblits is in the system PATH first,
+# and if not, fall back to the original hardcoded path.
+if command -v hhblits &> /dev/null; then
+  HHBLITS_CMD="hhblits"
+else
+  # This is the original path from the developer
+  HHBLITS_CMD="$BASE/hh-suite/build/bin/hhblits"
+fi
+
+################################################################################
+# Original Script Logic (changes to the execution paths for hhblits and predict_sc.py)
+#
+# The code below is the original workflow. All variables are now defined with
+# absolute paths by the header above.
+################################################################################
+
+
+#Write individual fasta files for all unique sequences
+if test -f $MSA; then
+	echo $MSA exists
+else
+	 $HHBLITS_CMD -i $FASTAWITHX -d $HHBLITSDB -E 0.001 -all -n 2 -oa3m $MSA
+fi
+
+
+#########Step2: Make MSA features#########
+#Here we also use "FASTAWITHX", the NCAA frames and features are mapped
+#later in the predict script when the MSA is sampled
+MSA_FEATS=$OUTDIR/msa_features.pkl
+if test -f $MSA_FEATS; then
+	echo $MSA_FEATS exists
+else
+	python3 $BASE/src/make_msa_seq_feats.py --input_fasta_path $FASTAWITHX \
+	--input_msas $MSA --outdir $OUTDIR
+fi
+
+#########Step3: Predict#########
+#The NCAAs will be saved to chain B in the prediction for easier visualisation
+python3 $BASE/src/predict_sc.py --predict_id $ID \
+--MSA_feats $MSA_FEATS \
+--fasta $FASTAFILE \
+--num_recycles $NUM_REC \
+--params $PARAMS \
+--outdir $OUTDIR