Add RODA flattening script

README.md

@@ -326,7 +326,8 @@ script.
 
 If you're using your own MSAs or MSAs from the RODA repository, make sure that
 the `alignment_dir` contains one directory per chain and that each of these
-contains alignments (.sto, .a3m, and .hhr) corresponding to that chain.
+contains alignments (.sto, .a3m, and .hhr) corresponding to that chain. You
+can use `scripts/flatten_roda.sh` to reformat RODA downloads in this way.
 
 Note that, despite its variable name, `mmcif_dir` can also contain PDB files 
 or even ProteinNet .core files. To emulate the AlphaFold training procedure, 

scripts/flatten_roda.sh

+#!/usr/bin/env sh
+#
+# Flattens a downloaded RODA database into the format expected by OpenFold
+# Args:
+#     roda_dir: 
+#           The path to the database you want to flatten. E.g. "roda/pdb" 
+#           or "roda/uniclust30". Note that, to save space, this script
+#           will empty this directory.
+#     output_dir:
+#           The directory in which to construct the reformatted data
+
+if [[ $# != 2 ]]; then
+    echo "usage: ./flatten_roda.sh <roda_dir> <output_dir>"
+    exit 1
+fi
+
+RODA_DIR=$1
+OUTPUT_DIR=$2
+
+DATA_DIR="${OUTPUT_DIR}/data"
+ALIGNMENT_DIR="${OUTPUT_DIR}/alignments"
+
+mkdir -p "${DATA_DIR}"
+mkdir -p "${ALIGNMENT_DIR}"
+
+for chain_dir in $(ls "${RODA_DIR}"); do
+    CHAIN_DIR_PATH="${RODA_DIR}/${chain_dir}"
+    for subdir in $(ls "${CHAIN_DIR_PATH}"); do
+        if [[ $subdir = "pdb" ]] || [[ $subdir = "cif" ]]; then
+            CHAIN_DATA_DIR="${DATA_DIR}/${chain_dir}"
+            mkdir -p "${CHAIN_DATA_DIR}"
+            mv "${CHAIN_DIR_PATH}/${subdir}"/* "${CHAIN_DATA_DIR}"
+        else
+            CHAIN_ALIGNMENT_DIR="${ALIGNMENT_DIR}/${chain_dir}"
+            mkdir -p "${CHAIN_ALIGNMENT_DIR}"
+            mv "${CHAIN_DIR_PATH}/${subdir}"/* "${CHAIN_ALIGNMENT_DIR}"
+        fi
+    done
+done
+
+NO_DATA_FILES=$(find "${DATA_DIR}" -type f | wc -l)
+if [[ $NO_DATA_FILES = 0 ]]; then
+    rm -rf ${DATA_DIR}
+fi