Basically I want to be able to invoke a given command, in this case mysql -uanon -ppwd -db mydb -e \"select count(*) from table1\". And then take this commands
mysql -uanon -ppwd -db mydb -e \"select count(*) from table1\"
You most likely want to use batch mode (-B) and disable column names (--disable-column-names) for non-interactive mysql output:
out=$(mysql -B -db mydb -uanon -ppwd --disable-column-names -e "select count(*) from table1";)