43 lines
1.4 KiB
Bash
Executable File
43 lines
1.4 KiB
Bash
Executable File
#!/bin/bash
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#
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# Copyright 2021 DeepMind Technologies Limited
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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# Downloads and unzips the PDB SeqRes database for AlphaFold.
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#
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# Usage: bash download_pdb_seqres.sh /path/to/download/directory
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set -e
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if [[ $# -eq 0 ]]; then
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echo "Error: download directory must be provided as an input argument."
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exit 1
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fi
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if ! command -v aria2c &> /dev/null ; then
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echo "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)."
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exit 1
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fi
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DOWNLOAD_DIR="$1"
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ROOT_DIR="${DOWNLOAD_DIR}/pdb_seqres"
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SOURCE_URL="ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
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BASENAME=$(basename "${SOURCE_URL}")
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mkdir --parents "${ROOT_DIR}"
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aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
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# Keep only protein sequences.
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grep --after-context=1 --no-group-separator '>.* mol:protein' "${ROOT_DIR}/pdb_seqres.txt" > "${ROOT_DIR}/pdb_seqres_filtered.txt"
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mv "${ROOT_DIR}/pdb_seqres_filtered.txt" "${ROOT_DIR}/pdb_seqres.txt"
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