snpalliance.sh

#!/bin/sh

#
# This script is a wrapper around the process that generates the Alliance TSV file.
#     snpalliance.sh 
#
# For each chromosome
#	. copy each Alliance vep/vcf ($SNP_ALLIANCE_INPUT) to the /data/loads/mgi/snpcacheload/output folder
#	. sort & uniq the file -> chr.tsv
#
# The TSV files remain static until this script is run again.
# This script should be run again if a new Alliance vep/vcf file is mirroed via mirror_wget/alliancegenome.org.variants
# This script needs to run on the SNP server:  bhmgidb05ld, bhmgidb03lp
#

cd `dirname $0` 

COMMON_CONFIG=Configuration

#
# Make sure the common configuration file exists and source it. 
#
if [ -f ${COMMON_CONFIG} ]
then
    . ${COMMON_CONFIG}
else
    echo "Missing configuration file: ${COMMON_CONFIG}"
    exit 1
fi

#
# Initialize the log file.
# open LOG in append mode and redirect stdout
#
LOG=${SNP_ALLIANCE_LOG}
rm -rf ${LOG}
>>${LOG}

cd ${CACHEDATADIR}

date >> ${LOG} 2>&1
echo "Process SNP Alliance Feed TSV files"  >> ${LOG} 2>&1
${PYTHON} ${SNPCACHELOAD}/snpalliance.py >> ${LOG} 2>&1
rm -rf *.tsv
for i in `ls snpalliance.output.*`
do
sort ${i} | uniq > ${i}.tsv
rm -rf ${i}
done
date >> ${LOG} 2>&1