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Full Discussion: Filter file by length, looking only at lines that don't begin with ">"
Top Forums Shell Programming and Scripting Filter file by length, looking only at lines that don't begin with ">" Post 302835661 by pathunkathunk on Monday 22nd of July 2013 11:20:54 PM
Old 07-23-2013
Filter file by length, looking only at lines that don't begin with ">"
I have a file that stores data in pairs of lines, following this format:
line 1: header (preceded by ">")
line 2: sequence

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

Gives me
Code:
>seq1 name
GATTGATGTTTGAGTTTTGGTTTTT
>seq2 name
>seq2 name
TTTTCTTC

How do I tell awk not to ignore lines beginning with ">"?
Last edited by Scrutinizer; 07-23-2013 at 02:55 AM.. Reason: code tags also for data samples. Do not use quote tags
 

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LEARN ABOUT MINIX

grep

GREP(1) 						      General Commands Manual							   GREP(1)

NAME

       grep - search a file for lines containing a given pattern

SYNOPSIS

       grep [-elnsv] pattern [file] ...

OPTIONS

       -e     -e pattern is the same as pattern

       -c     Print a count of lines matched

       -i     Ignore case

       -l     Print file names, no lines

       -n     Print line numbers

       -s     Status only, no printed output

       -v     Select lines that do not match

EXAMPLES

       grep mouse file	   # Find lines in file containing mouse

       grep [0-9] file	   # Print lines containing a digit

DESCRIPTION

       Grep  searches  one  or	more  files (by default, stdin) and selects out all the lines that match the pattern.  All the regular expressions
       accepted by ed and mined are allowed.  In addition, + can be used instead of * to mean 1 or more occurrences, ? can be used to mean 0 or  1
       occurrences,  and  |  can  be used between two regular expressions to mean either one of them.  Parentheses can be used for grouping.  If a
       match is found, exit status 0 is returned.  If no match is found, exit status 1 is returned.  If an error is detected,  exit  status  2	is
       returned.

SEE ALSO

       cgrep(1), fgrep(1), sed(1), awk(9).

																	   GREP(1)
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