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Top Forums Shell Programming and Scripting Filter (by max length) only lines not matching regex Post 302785149 by pathunkathunk on Monday 25th of March 2013 02:28:13 AM
Old 03-25-2013
Filter (by max length) only lines not matching regex

I have a large file of many pairs of sequences and their headers, which always begin with '>'
Quote:
>gi|abc| Species one
ATCAGGTATAATT
>gi|bcd| Species two
ATTTGATC
>gi|cdf| Species three
ATTTGATCT
I'm looking for help on how to retain only sequences (and their headers) below a certain length. So if min length was 10, output would be
Quote:
>gi|bcd| Species two
ATTTGATC
>gi|cdf| Species three
ATTTGATCT
I can filter by length, but I'm not sure how to exclude the header lines.
Code:
awk '{lines[NR] = $0} length($0) < 10 {print lines [NR-1]; print lines [NR]} ' file.name

 

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FMT(1)							    BSD General Commands Manual 						    FMT(1)

NAME
fmt -- simple text formatter SYNOPSIS
fmt [-Cr] [goal [maximum]] [name ...] fmt [-Cr] [-g goal] [-m maximum] [name ...] DESCRIPTION
fmt is a simple text formatter which reads the concatenation of input files (or standard input if none are given) and produces on standard output a version of its input with lines as close to the goal length as possible without exceeding the maximum. The goal length defaults to 65 and the maximum to 75. The spacing at the beginning of the input lines is preserved in the output, as are blank lines and interword spac- ing. In non raw mode, lines that look like mail headers or begin with a period are not formatted. -C instructs fmt to center the text. -g goal New way to set the goal length. -m maximum New way to set the maximum length. -r Raw mode; formats all lines and does not make exceptions for lines that start with a period or look like mail headers. fmt is meant to format mail messages prior to sending, but may also be useful for other simple tasks. For instance, within visual mode of the ex(1) editor (e.g., vi(1)) the command !}fmt will reformat a paragraph, evening the lines. SEE ALSO
mail(1), nroff(1) HISTORY
The fmt command appeared in 3BSD. BUGS
The program was designed to be simple and fast - for more complex operations, the standard text processors are likely to be more appropriate. BSD
May 29, 2007 BSD
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