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author | pfrommolt |
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date | Mon, 21 Nov 2011 08:12:19 -0500 |
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#!/bin/sh # fetchChromSizes - script to grab chrom.sizes from UCSC via either of: # mysql, wget or ftp # "$Id: fetchChromSizes,v 1.2 2009/03/26 18:40:09 hiram Exp $" usage() { echo "usage: fetchChromSizes <db> > <db>.chrom.sizes" echo " used to fetch chrom.sizes information from UCSC for the given <db>" echo "<db> - name of UCSC database, e.g.: hg18, mm9, etc ..." echo "" echo "This script expects to find one of the following commands:" echo " wget, mysql, or ftp in order to fetch information from UCSC." echo "Route the output to the file <db>.chrom.sizes as indicated above." echo "" echo "Example: fetchChromSizes hg18 > hg18.chrom.sizes" exit 255 } DB=$1 export DB if [ -z "${DB}" ]; then usage fi WGET=`type wget 2> /dev/null | sed -e "s/.* is //"` MYSQL=`type mysql 2> /dev/null | sed -e "s/.* is //"` FTP=`type ftp 2> /dev/null | sed -e "s/.* is //"` if [ -z "${WGET}" -a -z "${MYSQL}" -a -z "${FTP}" ]; then echo "ERROR: can not find any of the commands: wget mysql or ftp" usage fi DONE=0 export DONE if [ -n "${MYSQL}" ]; then echo "INFO: trying MySQL ${MYSQL} for database ${DB}" 1>&2 ${MYSQL} -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \ "SELECT chrom,size FROM chromInfo ORDER BY size DESC;" ${DB} if [ $? -ne 0 ]; then echo "WARNING: mysql command failed" 1>&2 else DONE=1 fi fi if [ "${DONE}" -eq 1 ]; then exit 0 fi if [ -n "${WGET}" ]; then echo "INFO: trying WGET ${WGET} for database ${DB}" 1>&2 tmpResult=chromInfoTemp.$$.gz ${WGET} \ "ftp://hgdownload.cse.ucsc.edu/goldenPath/${DB}/database/chromInfo.txt.gz" \ -O ${tmpResult} 2> /dev/null if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then echo "WARNING: wget command failed" 1>&2 rm -f "${tmpResult}" else zcat ${tmpResult} 2> /dev/null | cut -f1,2 | sort -k2nr rm -f "${tmpResult}" DONE=1 fi fi if [ "${DONE}" -eq 1 ]; then exit 0 fi if [ -n "${FTP}" ]; then echo "INFO: trying FTP ${FTP} for database ${DB}" 1>&2 tmpFtpRsp=fetchTemp.$$ echo "user anonymous fetchChromSizes@" > ${tmpFtpRsp} echo "cd goldenPath/${DB}/database" >> ${tmpFtpRsp} echo "get chromInfo.txt.gz ${tmpResult}" >> ${tmpFtpRsp} echo "bye" >> ${tmpFtpRsp} ${FTP} -u -n -i hgdownload.cse.ucsc.edu < ${tmpFtpRsp} > /dev/null 2>&1 if [ $? -ne 0 -o ! -s "${tmpResult}" ]; then echo "ERROR: ftp command failed" 1>&2 rm -f "${tmpFtpRsp}" "${tmpResult}" else zcat ${tmpResult} | cut -f1,2 | sort -k2nr rm -f "${tmpFtpRsp}" "${tmpResult}" DONE=1 fi fi if [ "${DONE}" -eq 0 ]; then echo "ERROR: sorry, attempt to fetch chrom.sizes has failed ?" 1>&2 exit 255 fi