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sialsaffarsialsaffar
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adding script to download data
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‎downloadData.sh‎

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#!/bin/bash
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## This script will create a Data/ directory in the download
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## the data used in this study each in its given sub-directory.
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shopt -s extglob
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# Set the download directory (same as working directory by default):
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workingdir="$( pwd )"
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outputdir=${workingdir}
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# Setting option for downloading only specific dataset (default: all):
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declare -a steps2run
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steps2run=(step1 step2 step3 step4 step5)
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runonlystep=""
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# Help menu:
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function usage() {
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echo "
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Download Data Help Section:
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===========================
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Usage: $0
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Or for more options:
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Example: $0 -o ~/path/to/my/directory/
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Optional arguments:
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-o|--outputdir <path> : Directory path for downloaded data
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--runonlystep <string> : Indicate a specific step to run (see below)
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-h|--help : Display this help message
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This script will download all 4 datasets by default. To download only
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a specific dataset, designate a step number when running the script.
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The following step numbers are valid options:
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step1 : downloads the Human Genome Dating atlas dataset from https://human.genome.dating/
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step2 : downloads recombination maps for GRCh37 from
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https://github.com/joepickrell/1000-genomes-genetic-maps
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step3 : downloads introgression map files from http://dical-admix.sourceforge.net/
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step4 : downloads population-specific annotation file from
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http://ftp.ensembl.org/pub/grch37/release-103/variation/gvf/homo_sapiens/
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step5 : download GRCh37 reference genome files from
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https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/
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"
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}
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if [ -z "$*" ]; then usage ; exit 1 ; fi
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# Parsing command-line arguments:
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OPTIONS=`getopt -o o:h --long outputdir:,runonlystep:,help -n 'download error' -- "$@"`
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if [ $? != 0 ]; then echo " " ; echo "Could not parse options (see above) ..." >&2 ; usage ; exit 1 ; fi
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eval set -- "$OPTIONS"
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while true ; do
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case "$1" in
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-o|--outputdir)
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case "$2" in
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-*) echo "Please designate an output directory when using -o"; usage; exit 1 ;;
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*) outputdir=$2 ; shift 2 ;;
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esac ;;
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--runonlystep)
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case "$2" in
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-*) echo "Please designate the code4Rice3K step to execute"; usage; exit 1 ;;
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*) runonlystep=$2 ; shift 2 ;;
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esac ;;
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-h|--help)
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usage; exit 1 ;;
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--) shift ; break ;;
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*) echo "Unknown option or error" ; usage ; exit 1 ;;
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esac
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done
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# Control which step to run:
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if [[ $runonlystep != '' ]] ; then
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steps2run=($runonlystep)
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fi
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# Step 0
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#
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echo ""
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echo "=============================================================================="
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echo " Downloading datasets for the Wang etal., 2022 paper ..."
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echo "=============================================================================="
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echo ""
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runstep1=0
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runstep2=0
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runstep3=0
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runstep4=0
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runstep5=0
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for step in ${steps2run[@]} ; do
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if [[ $step == "step1" ]] ; then runstep1=1 ; fi
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if [[ $step == "step2" ]] ; then runstep2=1 ; fi
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if [[ $step == "step3" ]] ; then runstep3=1 ; fi
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if [[ $step == "step4" ]] ; then runstep4=1 ; fi
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if [[ $step == "step5" ]] ; then runstep5=1 ; fi
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done
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if [ ! -d "$outputdir" ] ; then
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echo ""
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echo "... new output directory $outputdir will be created in your working directory."
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mkdir $outputdir
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fi
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cd $outputdir
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mkdir -p Atlas Recombination Introgression Populations Reference
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# Step 1
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if [[ $runstep1 == 1 ]]; then
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echo ""
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echo "=============================================================================="
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echo "Step 1 Downlowding atlas SNP dating files ..."
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echo "=============================================================================="
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echo ""
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cd ${workingdir}
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cd ${outputdir}/Atlas
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for i in {1..22}; do
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if [[ ! -e atlas.chr${i}.csv ]]; then
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wget https://human.genome.dating/bulk/atlas.chr${i}.csv.gz && gunzip atlas.chr${i}.csv.gz
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fi
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done
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echo "Atlas files downloaded"
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echo ""
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fi
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# Step 2
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if [[ $runstep2 == 1 ]]; then
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echo ""
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echo "=============================================================================="
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echo "Step 2 Downlowding GRCH37 recombination maps ..."
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echo "=============================================================================="
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echo ""
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cd ${workingdir}
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cd ${outputdir}/Recombination
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if [[ ! -e HapmapII_GRCh37_RecombinationHotspots.tar.gz ]]; then
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wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20110106_recombination_hotspots/HapmapII_GRCh37_RecombinationHotspots.tar.gz && tar -xzvf HapmapII_GRCh37_RecombinationHotspots.tar.gz
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fi
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echo "Recombination maps downloaded"
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echo ""
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fi
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# Step 3
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if [[ $runstep3 == 1 ]]; then
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echo ""
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echo "=============================================================================="
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echo "Step 3 Downlowding Neanderthal introgression files ..."
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echo "=============================================================================="
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echo ""
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cd ${workingdir}
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cd ${outputdir}/Introgression
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echo "
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Actually, I couldn't put a script here to download this data directly.
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The Neanderthal introgression files from Steinrucken et al., 2018
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are hosted on a google drive. You can download it yourself following
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this link here:
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https://drive.google.com/drive/folders/175ae-y9Q9Q6FQN6kQS6iGduzeAdHQZXY
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"
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echo ""
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fi
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# Step 4
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if [[ $runstep4 == 1 ]]; then
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echo ""
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echo "=============================================================================="
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echo "Step 4 Downlowding population-specific annotations ..."
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echo "=============================================================================="
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echo ""
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cd ${workingdir}
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cd ${outputdir}/Populations
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if [[ ! -e 1000GENOMES-phase_3.gvf ]]; then
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wget http://ftp.ensembl.org/pub/grch37/release-103/variation/gvf/homo_sapiens/1000GENOMES-phase_3.gvf.gz && gunzip 1000GENOMES-phase_3.gvf.gz
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fi
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echo "Population-specific GVF file downloaded"
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echo ""
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fi
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# Step 5
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if [[ $runstep5 == 1 ]]; then
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echo ""
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echo "=============================================================================="
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echo "Step 5 Downlowding GRCh37 reference genome ..."
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echo "=============================================================================="
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echo ""
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cd ${workingdir}
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cd ${outputdir}/Reference
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if [[ ! -e GCF_000001405.25_GRCh37.p13_genomic.fna ]]; then
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wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.fna.gz && gunzip GCF_000001405.25_GRCh37.p13_genomic.fna.gz
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fi
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echo "Referece genome file downloaded"
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echo ""
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fi
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echo ""
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echo "=============================================================================="
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echo "Files downloaded."
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echo "=============================================================================="
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echo ""
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exit
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