UNIX for Dummies Questions & Answers

Or maybe just:

Code:

sed 's/[AGCT]\{2,\}/ /g' file

Code:

awk '$2!~/^[ATGC]$/ {$2=" "} $3!~/^[ATGC]$/ {$3=" "} {print}'

explanations:

for each line awk does
'condition {action} condition {action} ...'

The ERE /^[ATGC]$/ matches exact an A or T or G or C
The EREs (^A$|^T$|^G$|^C$) or ^(A|T|G|C)$ do the same, are more general, but perhaps a bit slower than the character set.
ERE stands for extended regular expression.

If column 2 is not the ERE then set column 2 to " "
If column 3 is not the ERE then set column 3 to " "
Always print the whole line ($0)