Multi-conditional IF - awk


 
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# 1  
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
# 2  
Old 03-21-2018
Note that = is an assignment operator. It assigns the value of right side expression to left side.

But == is an equal to operator. It compares the value of both sides. Hence you have to use == in your if condition.
This User Gave Thanks to Yoda For This Post:
# 3  
Old 03-21-2018
Quote:
Originally Posted by Yoda
Note that = is an assignment operator. It assigns the value of right side expression to left side.

But == is an equal to operator. It compares the value of both sides. Hence you have to use == in your if condition.
Thanks Yoda, works like a charm Smilie
# 4  
Old 03-21-2018
Code:
awk '
{
if (str ~ ":" $6 ":") $6=toupper($6);
print $0;
}' str=":a:c:g:t:" datafile

or
Code:
awk '$6=toupper($6)' datafile


Last edited by rdrtx1; 03-21-2018 at 05:12 PM..
This User Gave Thanks to rdrtx1 For This Post:
# 5  
Old 03-21-2018
Based on your sample, where there is NO other field containing "a","c","g", or "t", this could work:
Code:
sed 'y/acgt/ACGT/' file

This User Gave Thanks to RudiC For This Post:
# 6  
Old 03-21-2018
Quote:
Originally Posted by rdrtx1
Code:
awk '
{
if (str ~ ":" $6 ":") $6=toupper($6);
print $0;
}' str=":a:c:g:t:" datafile

or
Code:
awk '$6=toupper($6)' datafile

Nice Rdtrx1! A little more limited than my script but fine for this purpose
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