SRA download script

ascp_get.sh

#!/bin/sh

if [ $# -ne 1 ]
then
    cat << EOF

usage: $0 <list of SRA location, name (whitespace seperated)>

For example, make a file called sra.txt and add this to it:

/sra/sra-instant/reads/ByExp/sra/SRX/SRX243/SRX243479 orang_kiki
/sra/sra-instant/reads/ByExp/sra/SRX/SRX243/SRX243480 orang_kiki
/sra/sra-instant/reads/ByExp/sra/SRX/SRX243/SRX243476 orang_napoleon
/sra/sra-instant/reads/ByExp/sra/SRX/SRX243/SRX243475 orang_napoleon

Then execute:

$0 sra.txt

You may need to edit the following line:

ascp=$HOME/aspera/connect

to point to your aspera installation.

EOF

    exit 65
fi

ascp=$HOME/aspera/connect

IFS=$'\n'
for line in `cat $1`
do
    filepath=`echo $line | awk '{print $1}'`
    outdir=`echo $line | awk '{print $2}'`

    if [ ! -d $outdir ]
    then
        echo "$outdir does not exist, creating directory"
        mkdir $outdir
    fi

    if [ ! -d $outdir ]
    then
        echo "failed to create directory: $outdir"
        exit 1
    fi

    $ascp/bin/ascp -i $ascp/etc/asperaweb_id_dsa.putty -QTr -l500M anonftp@ftp-private.ncbi.nlm.nih.gov:$filepath $outdir
done