The server had a setup in which a cronjob was used to dump output of top command to a directory accessible via http once every 5 minutes. To get rid of the logs and also to prune mysql logs the following script was made.
#! /bin/sh
LOGGER_PATH='/usr/local/apache/htdocs/top/'
N_DAY=3
MYSQL_DATA_DIR='/var/lib/mysql'
LOGSTOKEEP=3
################################################
#find and delete all files
#in logger path older than n days
################################################
find $LOGGER_PATH -mtime +$N_DAY -exec rm -f {} \;
################################################
#mysql pruner section.
#flush logs first,
#find the last filename
#and purge binary logs upto that
################################################
#mysql flush logs here
FILENAMES=`ls $MYSQL_DATA_DIR | grep -e "^mysql-bin.0\+[[:digit:]]\+$"|sort|tail -n $LOGSTOKEEP`
LINECOUNT=`echo $FILENAMES|wc -w`
#linecount will be lesser than or equal to the number of logs we want to keep
if [ $LINECOUNT -lt $LOGSTOKEEP ]; then
echo "$LOGSTOKEEP files were not found. So no purge is being done."
else
LASTFILENAME=`echo $FILENAMES|cut -d' ' -f 1`
#do purge upto lastfilename
fi
exit
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