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Replacing "." with "GG" in a certain column of a file that has heading

 
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# 1  
Old 12-12-2014
Replacing "." with "GG" in a certain column of a file that has heading
Hi, all, I have a file that looks like:
Code:
## XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX                              
## YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY                                            
#AA    AB    AC    AD    AE    AF    AG    AH    AI    AJ    AK    AL
20    60039    60039    T    C    1000    PASS    .    .    0|0    0|0    0|0
20    60097    60097    G    A    999    PASS    .    .    0|0    0|0    0|0

The file has two lines starting with ## - heading lines (## XXX and ## YYY). Third line from above starting with # - indicate names of the columns (AA, AB etc). And the rest of the lines - are values.

I need to replace "." to "GG" in the 9th column AI.
Heading should stay unchanged. File is lets say, tab-delimited.

Thank u for ur suggestion!
best, kush
Last edited by Scrutinizer; 12-13-2014 at 09:13 AM.. Reason: Modified incorrectly put code tags
# 2  
Old 12-12-2014
Try this (verbose) awk code:
Code:
awk -F'\t' '
    NR < 4 { print }
    NR > 3 {  $9="GG"; print }
' OFS='\t' file

This User Gave Thanks to junior-helper For This Post:
kush
# 3  
Old 12-12-2014
Try
Code:
awk '{sub (/^\.$/,"GG",$9)}1' file

This User Gave Thanks to RudiC For This Post:
kush
# 4  
Old 12-12-2014
Quote:
Originally Posted by junior-helper
Try this (verbose) awk code:
Code:
awk -F'\t' '
    NR < 4 { print }
    NR > 3 {  $9="GG"; print }
' OFS='\t' file

thank you a lot!!!
# 5  
Old 12-13-2014
Quote:
Originally Posted by RudiC
Try
Code:
awk '{sub (/^\.$/,"GG",$9)}1' file

thanks a lot for all your quick help!
best, kush
# 6  
Old 12-13-2014
Ignoring the comment lines:
Code:
awk '$1!~/^#/ && $9=="."{$9="GG"}1' FS='\t' OFS='\t file

 
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