How to modify lines without certain patterns?

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12-13-2012

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How to modify lines without certain patterns?

I have file like this:

Code:

rs111 A T 0.9 0.8 ...
rs112 AT T 0.8 0.2 ...
rs113 G CT 0.9 0.1...

I wish to replace all the NONE "A" or "T" or "G" or "C" values in column 3 and column 4 to " ", how can I do this?

thanks!

Last edited by Scrutinizer; 12-14-2012 at 04:13 AM.. Reason: code tags

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12-13-2012

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Checking column 3 & replacing with " "

Code:

awk '$3 !~ /(^A$|^T$|^G$|^C$)/ { $3=" "; print $0 } $3 ~ /(^A$|^T$|^G$|^C$)/ { print $0; } ' infile

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12-14-2012

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Quote:

Originally Posted by bipinajith

Checking column 3 & replacing with " "

Code:

awk '$3 !~ /(^A$|^T$|^G$|^C$)/ { $3=" "; print $0 } $3 ~ /(^A$|^T$|^G$|^C$)/ { print $0; } ' infile

thanks for this! It works! One issue my file is very huge, it's about 11G. I have two columns I need to modify, while keep the rest the same. Ran this code twice to write in new files really takes time. Is there a way to speed it up? Or just modify the original file?

Another question is I am really new for unix, may I know what does print $0 mean?

thanks!

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12-14-2012

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Quote:

Originally Posted by luoruicd

I have file like this:
rs111 A T 0.9 0.8 ...
rs112 AT T 0.8 0.2 ...
rs113 G CT 0.9 0.1...

I wish to replace all the NONE "A" or "T" or "G" or "C" values in column 3 and column 4 to " ", how can I do this?

thanks!

i dont understand the above highlighted statement. can you give more input and the expected output.

$0 - indicates the current line (processing line) in awk

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12-14-2012

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For example:
my original file looks like this:

Code:

rs111 A T 0.9 0.8 ...
rs112 AT T 0.8 0.2 ...
rs113 G CT 0.9 0.1...

I want to modify column 2 and column3. In column 2, line2 it is not A or T or G or C, then I want to change it to " ", the same for column3, line3

The output file should be:

Code:

rs111 A T 0.9 0.8 ...
rs112   T 0.8 0.2 ...
rs113 G   0.9 0.1...

Last edited by Scrutinizer; 12-14-2012 at 04:13 AM.. Reason: code tags

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12-14-2012

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try this..

Code:

 
awk '$2!~/(^A$|^T$|^G$|^C$)/{$2=" "}$3!~/(^A$|^T$|^G$|^C$)/{$3=" "}{print}' inputfile

---------- Post updated at 11:29 AM ---------- Previous update was at 11:27 AM ----------

Code:

 
perl -lane 'if($F[1]!~/(^A$|^T$|^G$|^C$)/){$F[1]=" ";}if($F[2]!~/(^A$|^T$|^G$|^C$)/){$F[2]=" ";}print join " ",@F;' input.txt

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thanks! Unix code works, but not perl. I never used perl, so will just go with the unix one.

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