You can use awk to change the field separator in a data stream:

$ cat foo
a,b,c,d,e,f
a,b,c,d,e,f
$ awk 'BEGIN { FS = ","; OFS = ".."; } { $1 = $1; print }' foo
a..b..c..d..e..f
a..b..c..d..e..f

(You just have to touch one of the fields to get it to process the line.)