Filter file by length, looking only at lines that don't begin with ">"

Shell Programming and Scripting
1

I have a file that stores data in pairs of lines, following this format:
line 1: header (preceded by ">")
line 2: sequence

Example.txt:

>seq1 name
GATTGATGTTTGAGTTTTGGTTTTT
>seq2 name
TTTTCTTC

I want to filter out the sequences and corresponding headers for all sequences that are less than 11 characters. Desired output:

>seq2 name
TTTTCTTC

I can search each line for lines less than 11 characters, and print that line along with the header. The problem I'm having is ignoring the headers (i.e. lines beginning with ">") when I do the length search.

For example

awk '{lines[NR] = $0} length($0) < 11 {print lines [NR-1]; print lines [NR]} ' example.txt

Gives me

>seq1 name
GATTGATGTTTGAGTTTTGGTTTTT
>seq2 name
>seq2 name
TTTTCTTC

How do I tell awk not to ignore lines beginning with ">"?

2

try..

 
awk '{lines[NR] = $0}!/>/&&length($0) < 11 {print lines [NR-1]; print lines [NR]} ' example.txt
2 Likes
3

That does the trick, thanks.