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Cut & awk

 
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# 1  
Old 07-20-2015
Cut & awk
I am using the following code to modify all odd lines in a file:
Code:
awk 'NR % 2 { print } !(NR % 2)' FWD-1.fas | cut -c5-600

I however, do not want cut to affect the odd lines
Any help?
# 2  
Old 07-20-2015
Don't use cut. awk equivalent is substr($0,5,595)

try:
Code:
awk '!(NR%2) { print substr($0,5,595); next; } 1' FWD-1.fas

This User Gave Thanks to neutronscott For This Post:
Xterra
# 3  
Old 07-20-2015
Hi Xterra,
The pipeline you have is logically equivalent to:
Code:
cut -c5-600 FWD-1.fas

but runs slower since you're reading and writing the file twice instead of just once.

Hi Neutronscott,
I think you have an off-by-1 error in the substring. What you have would emulate cut -c5-599

I would try something like:
Code:
awk '!(FNR % 2) {$0 = substr($0, 5, 596)} 1' FWD-1.fas

These 2 Users Gave Thanks to Don Cragun For This Post:
neutronscott Xterra
# 4  
Old 07-20-2015
oy. darn 1-index. Thanks, Don.

but yes, everything outputted by awk goes to cut. cut doesn't have logic like awk does. But awk can determine if it's an odd line and also skip the first 5 characters.

the 1 at the end is shorthand for {print $0}, so that lines that weren't modified will still be printed as they were.
This User Gave Thanks to neutronscott For This Post:
Xterra
 
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