Bash: cutting a delimited fragment of each string

Question

I have a file containing lines that look like this:

GTTCAGAGTTCTACAGTCCGACGATCGGATGAGNNNNNN
GTTCAGAGTTCTACAGTCCGACGATCTCCGAGTNNNNNN
GTTCAGAGTTCTACAGTCCGACGATCCTTATATNNNNNN
GTTCAGAGTTCTACAGTCCGACGATCGAAGTGCNNNNNN
GTTCAGAGTTCTACAGTCCGACGATCAAGTTTTNNNNNN
GTTCAGAGTTCTACAGTCCGACGATCCGACGAANNNNNN

I want to remove the first 26 and final 6 characters from each line. I haven't been able to write a good regular expression to accomplish that using vi, but I'm not sure what else to do. Any suggestions?

Thanks!

Regex is not suitable for all problems. It's a heavy hammer for a small problem like grabbing a static set of bytes from a list of strings. — PaulProgrammer, Dec 03 '13 at 23:16
possible duplicate of [What linux shell command returns a part of a string?](http://stackoverflow.com/questions/219402/what-linux-shell-command-returns-a-part-of-a-string), or *why would you use regex when you know exactly how many characters you want to cut?!? — dmckee --- ex-moderator kitten, Dec 04 '13 at 00:31

Federico Giorgi · Accepted Answer · 2013-12-03T23:17:48.380

3

Try with grep.

This will keep the last 13 characters and then the first 7, returning only the matching characters (-o) with the Perl-compliant -P flag:

grep -oP ".{13}$" foo.txt | grep -oP ".{7}"

edited Dec 03 '13 at 23:17

answered Dec 03 '13 at 23:10

Federico Giorgi

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don't forget to mark it the correct one when you can, Forest. – Plasmarob Dec 03 '13 at 23:15
His example lines are 39 characters. What if some were 50 characters? Given known conditions `unknown length = 26 + unknown segment + 6` Thats 1 equation, 2 unknowns. Yet you solve it. – Dec 03 '13 at 23:31

score 2 · Answer 2 · answered Dec 03 '13 at 23:14

2

If your file name is foo you can use cut to grab out the range of chars you want:

$ cut -c27-33 foo

This produces:

GGATGAG
TCCGAGT
CTTATAT
GAAGTGC
AAGTTTT
CGACGAA

answered Dec 03 '13 at 23:14

PaulProgrammer

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score 1 · Answer 3 · answered Dec 03 '13 at 23:15

1

cut can take a character range, if the lines are a fixed size (they appear to each be 39 characters)

cut -c27-33 file.txt

answered Dec 03 '13 at 23:15

chepner

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Bash: cutting a delimited fragment of each string

3 Answers3