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Full Discussion: Multi-conditional IF - awk
Top Forums Shell Programming and Scripting Multi-conditional IF - awk Post 303014831 by Geneanalyst on Wednesday 21st of March 2018 03:36:12 PM
Old 03-21-2018
Question Multi-conditional IF - awk
I have a 6 column array with 2 million rows that looks like this:
Code:
1 1089699 rs6686003 G A g     
1 1090557 rs7553429 A C c     
1 1094738 rs4970362 A G a     
1 1099342 rs9660710 A C c     
1 1106473 rs4970420 G A a     
1 1108637 rs4970421 G A g     
1 1119858 rs1320565 C T c     
1 1120431 rs1320571 G A A

I need to change all lower case letters in the 6th column to uppercase. I wrote the following script, but all it is doing is changing every value in the 6th column to "A"

Code:
awk '{ 
if ($6="a") $6="A"; 
else if ($6="c") $6="C"; 
else if ($6="g") $6="G"; 
else if ($6="t") $6="T"; 
print $0;
}'

This is what I'm getting:

Code:
1 1089699 rs6686003 G A A
1 1090557 rs7553429 A C A
1 1094738 rs4970362 A G A
1 1099342 rs9660710 A C A
1 1106473 rs4970420 G A A
1 1108637 rs4970421 G A A
1 1119858 rs1320565 C T A
1 1120431 rs1320571 G A A

I have Ubuntu 16.04 LTS. Any help would be greatly appreciated.
Last edited by Geneanalyst; 03-21-2018 at 04:38 PM.. Reason: added info
 

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LEARN ABOUT REDHAT

igawk

IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME

       igawk - gawk with include files

SYNOPSIS

       igawk [ all gawk options ] -f program-file [ -- ] file ...
       igawk [ all gawk options ] [ -- ] program-text file ...

DESCRIPTION

       Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).

       AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like

	      @include getopt.awk

       in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.

OPTIONS

       See gawk(1) for a full description of the AWK language and the options that gawk supports.

EXAMPLES

       cat << EOF > test.awk
       @include getopt.awk

       BEGIN {
	    while (getopt(ARGC, ARGV, "am:q") != -1)
		 ...
       }
       EOF

       igawk -f test.awk

SEE ALSO

       gawk(1)

       Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.

AUTHOR

       Arnold Robbins (arnold@skeeve.com).

Free Software Foundation					    Nov 3 1999								  IGAWK(1)
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