2 echo 'regionCounts.sh: version 1.0'
6 cachepages="--cache "$3
10 echo 'usage: regionCounts.sh partitionfile datalist.file [cachevalue]'
12 echo 'where the datalist file is a comma-delimited list of prefix and rds-files'
15 arguments=$1' '$2' '$cachepages
16 python $ERANGEPATH/recordLog.py regionCounts.log regionCounts.sh "with parameters: $arguments"
19 prefix=`echo $line | cut -f 1 -d ','`
20 rds=`echo $line | cut -f 2 -d ','`
22 python $ERANGEPATH/regionCounts.py $1 $rds $prefix.partcount --force --nomerge --rpkm $cachepages
24 echo "could not find $rds - skipping"
25 python $ERANGEPATH/recordLog.py regionCounts.log regionCounts.sh "could not find $rds - skipping"