edited the code to the following. This will save the data ~ 1x / second (I don't really care about a slight cumalative error in this since it's constant - it'll just be a systematic error in my frequency scaling)

global SERPORT
set SERPORT [open "/dev/ttyS0" "w+"]

fconfigure $SERPORT -mode 9600,n,8,1 -handshake none -buffering line

proc run_query { command } {
global SERPORT

puts $SERPORT "$command"
flush $SERPORT
gets $SERPORT line

return $line
}

#@puts [run_query "BEEP?"]

         set filename "/users/dmass/scripts/test.txt"
         set fileId [open $filename "w"]

 for { set i 1 } { $i <= 2000 } { incr i } {
#       puts "[clock format [clock seconds]]\t[run_query "TEC:T?"]"
                puts $fileId [run_query "TEC:T?"]
        after 1000
        }
close $fileId