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I would like to replace "CC" with "C" and "AA" with A" in a particular column of Tab delimited file (using awk probably).

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awk -F'\t' -vOFS='\t' '{ gsub("CC", "C", $1) ; gsub("AA", "A", $1) ; print }'

Replace $1 with the column that you wish to modify.

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In case the delimiter has to be kept, a -vOFS='\t' option may be added. –  manatwork Jun 14 '12 at 10:18
 
@manatwork Good point, added. –  Chris Down Jun 14 '12 at 10:20
 
fantastic! works as per usual!!! –  alex Jun 14 '12 at 10:51
 
Some versions of awk don't have a gsub function. How would you do it then? Can sed be used instead? –  rahmu Jun 14 '12 at 13:33
 
@rahmu - gsub() has been defined by POSIX for over 20 years, so my suggestion would be to get a version of awk that isn't downright awful ;-) –  Chris Down Jun 14 '12 at 13:40
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