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#!/bin/bash |
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if ! command -v curl &> /dev/null |
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then |
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echo "'curl' could not be found. You need to install 'curl' for this script to work." |
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exit 1 |
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fi |
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PROGNAME=$0 |
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BASE_URL="https://files.rcsb.org/download" |
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usage() { |
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cat << EOF >&2 |
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Usage: $PROGNAME -f <file> [-o <dir>] [-c] [-p] |
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-f <file>: the input file containing a comma-separated list of PDB ids |
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-o <dir>: the output dir, default: current dir |
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-c : download a cif.gz file for each PDB id |
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-p : download a pdb.gz file for each PDB id (not available for large structures) |
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-a : download a pdb1.gz file (1st bioassembly) for each PDB id (not available for large structures) |
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-x : download a xml.gz file for each PDB id |
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-s : download a sf.cif.gz file for each PDB id (diffraction only) |
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-m : download a mr.gz file for each PDB id (NMR only) |
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-r : download a mr.str.gz for each PDB id (NMR only) |
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EOF |
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exit 1 |
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} |
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download() { |
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url="$BASE_URL/$1" |
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out=$2/$1 |
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echo "Downloading $url to $out" |
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curl -s -f $url -o $out || echo "Failed to download $url" |
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} |
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listfile="" |
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outdir="." |
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cif=false |
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pdb=false |
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pdb1=false |
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xml=false |
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sf=false |
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mr=false |
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mrstr=false |
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while getopts f:o:cpaxsmr o |
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do |
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case $o in |
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(f) listfile=$OPTARG;; |
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(o) outdir=$OPTARG;; |
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(c) cif=true;; |
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(p) pdb=true;; |
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(a) pdb1=true;; |
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(x) xml=true;; |
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(s) sf=true;; |
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(m) mr=true;; |
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(r) mrstr=true;; |
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(*) usage |
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esac |
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done |
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shift "$((OPTIND - 1))" |
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if [ "$listfile" == "" ] |
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then |
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echo "Parameter -f must be provided" |
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exit 1 |
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fi |
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contents=$(cat $listfile) |
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IFS=',' read -ra tokens <<< "$contents" |
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for token in "${tokens[@]}" |
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do |
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if [ "$cif" == true ] |
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then |
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download ${token}.cif.gz $outdir |
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fi |
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if [ "$pdb" == true ] |
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then |
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download ${token}.pdb.gz $outdir |
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fi |
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if [ "$pdb1" == true ] |
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then |
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download ${token}.pdb1.gz $outdir |
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fi |
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if [ "$xml" == true ] |
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then |
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download ${token}.xml.gz $outdir |
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fi |
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if [ "$sf" == true ] |
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then |
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download ${token}-sf.cif.gz $outdir |
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fi |
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if [ "$mr" == true ] |
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then |
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download ${token}.mr.gz $outdir |
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fi |
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if [ "$mrstr" == true ] |
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then |
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download ${token}_mr.str.gz $outdir |
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fi |
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done |
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