Showing posts with label awk extended regular expressions filter gsub gawk. Show all posts
Showing posts with label awk extended regular expressions filter gsub gawk. Show all posts

Wednesday, June 4, 2014

filter strings with awk, extended regular expressions

I've been wanting to filter out a DNA sequence within a line of text using awk, and have been unsuccessful. I was trying:

gawk '{gsub(/[ACTG]{10,}/,""); print}'

which I expected to work, but it was not. I've found that gawk (GNU awk) has an extra setting that allows this syntax:

gawk --re-interval '{gsub(/[ACTG]{10,}/,""); print}'

This works.
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