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Remove lines based on column value

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# 1  
Old 12-19-2011
Remove lines based on column value
Hi All,
I just need a quick fix here. I need to delete all lines containing "." in the 6th column.

Input:
Code:
1       1055498 .       G       T       5.46    .       
1       1902377 .       C       T       7.80    .       
1       1031540 .       A       G       34.01   PASS    
1       1032841 .       G       T       14.92   LowQual

Desired Output:
Code:
1       1031540 .       A       G       34.01   PASS    
1       1032841 .       G       T       14.92   LowQual

---------- Post updated at 07:30 PM ---------- Previous update was at 07:29 PM ----------

I would also like to know how to replace the "." with "-1" if possible
Last edited by zxmaus; 12-19-2011 at 09:45 PM..
# 2  
Old 12-19-2011
Quote:
Originally Posted by Hkins552
Hi All,
I just need a quick fix here. I need to delete all lines containing "." in the 6th column.

Input:
1 1055498 . G T 5.46 .
1 1902377 . C T 7.80 .
1 1031540 . A G 34.01 PASS
1 1032841 . G T 14.92 LowQual

Desired Output:
1 1031540 . A G 34.01 PASS
1 1032841 . G T 14.92 LowQual
Code:
awk '$7 == "." { next } { print }' "$file"

Quote:

---------- Post updated at 07:30 PM
---------- Previous update was at 07:29 PM ----------

I would also like to know how to replace the "." with "-1" if possible
Code:
awk '$7 == "." { $7 = "-1" } { print }' "$file"

These 2 Users Gave Thanks to cfajohnson For This Post:
AlexL ryran
# 3  
Old 12-20-2011
Quote:
Originally Posted by Hkins552
I would also like to know how to replace the "." with "-1" if possible
In case you're referring to the "." in the 3rd field:

Code:
awk '$7 == "." {next}; $3 == "." {$3 = "-1"} {print}' file

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