48 lines
1.4 KiB
Bash
Executable File
48 lines
1.4 KiB
Bash
Executable File
#!/usr/bin/env sh
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#
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# Flattens a downloaded RODA database into the format expected by OpenFold
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# Args:
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# roda_dir:
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# The path to the database you want to flatten. E.g. "roda/pdb"
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# or "roda/uniclust30". Note that, to save space, this script
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# will empty this directory.
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# output_dir:
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# The directory in which to construct the reformatted data
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if [[ $# != 2 ]]; then
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echo "usage: ./flatten_roda.sh <roda_dir> <output_dir>"
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exit 1
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fi
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RODA_DIR=$1
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OUTPUT_DIR=$2
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DATA_DIR="${OUTPUT_DIR}/data"
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ALIGNMENT_DIR="${OUTPUT_DIR}/alignments"
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mkdir -p "${DATA_DIR}"
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mkdir -p "${ALIGNMENT_DIR}"
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for chain_dir in $(ls "${RODA_DIR}"); do
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CHAIN_DIR_PATH="${RODA_DIR}/${chain_dir}"
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for subdir in $(ls "${CHAIN_DIR_PATH}"); do
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if [[ ! -d "$subdir" ]]; then
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echo "$subdir is not directory"
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continue
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elif [[ -z $(ls "${subdir}")]]; then
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continue
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elif [[ $subdir = "pdb" ]] || [[ $subdir = "cif" ]]; then
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mv "${CHAIN_DIR_PATH}/${subdir}"/* "${DATA_DIR}"
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else
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CHAIN_ALIGNMENT_DIR="${ALIGNMENT_DIR}/${chain_dir}"
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mkdir -p "${CHAIN_ALIGNMENT_DIR}"
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mv "${CHAIN_DIR_PATH}/${subdir}"/* "${CHAIN_ALIGNMENT_DIR}"
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fi
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done
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done
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NO_DATA_FILES=$(find "${DATA_DIR}" -type f | wc -l)
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if [[ $NO_DATA_FILES = 0 ]]; then
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rm -rf ${DATA_DIR}
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fi
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