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53 lines
1.7 KiB
Bash
Executable File
53 lines
1.7 KiB
Bash
Executable File
#!/bin/bash
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#
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# Copyright 2021 AlQuraishi Laboratories
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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 .cif files matching the RODA alignments. Outputs a list of
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# RODA alignments for which .cif files could not be found..
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if [[ $# != 2 ]]; then
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echo "usage: ./download_roda_pdbs.sh <out_dir> <roda_pdb_alignment_dir>"
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exit 1
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fi
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OUT_DIR=$1
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RODA_ALIGNMENT_DIR=$2
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if [[ -d $OUT_DIR ]]; then
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echo "${OUT_DIR} already exists. Download failed..."
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exit 1
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fi
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SERVER=snapshotrsync.rcsb.org # RCSB server name
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PORT=873 # port RCSB server is using
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rsync -rlpt -v -z --delete --port=$PORT $SERVER::20220103/pub/pdb/data/structures/divided/mmCIF/ $OUT_DIR 2>&1 > /dev/null
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for f in $(find $OUT_DIR -mindepth 2 -type f); do
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mv $f $OUT_DIR
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BASENAME=$(basename $f)
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gunzip "${OUT_DIR}/${BASENAME}"
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done
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find $OUT_DIR -mindepth 1 -type d,l -delete
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for d in $(find $RODA_ALIGNMENT_DIR -mindepth 1 -maxdepth 1 -type d); do
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BASENAME=$(basename $d)
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PDB_ID=$(echo $BASENAME | cut -d '_' -f 1)
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CIF_PATH="${OUT_DIR}/${PDB_ID}.cif"
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if [[ ! -f $CIF_PATH ]]; then
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echo $d
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fi
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done
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