Trimming ends Post: 302947485

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Top Forums UNIX for Dummies Questions & Answers Trimming ends Post 302947485 by Xterra on Thursday 18th of June 2015 09:09:25 AM

06-18-2015

Registered User

Trimming ends

My files look like this

Quote:

>GHXCZCC01AJ8CJ
ACGTGCGTGGGAAATTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTACGCCCCGGGGC
>GHXCZCC01APUO5
ACGTGCGTGGGAAAT-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTACCCGGGGCGA
>GHXCZCC01AQSRP
ACGTGCGTGGGAAATTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTAGATTTTCTGGGGCCCCGGGG
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTATAGCTGGATTTTCTGGGACGCCCCGGGGTGC

I need to remove the sequence GGGAAA and anything before that

I also need to remove the sequence AGCCCTA and anything after that

So I will end up with something like this

Quote:

>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGA
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGC
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGG
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTG
>GHXCZCC01AQSRP
TTGATGTTGCCC

The left side is done but I cannot get the right side correctly. I would like to use one AWK script to accomplish the whole think instead of multiple steps
Thanks for any help!

Xterra

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LEARN ABOUT LINUX

tzselect

TZSELECT(8)						    Linux System Administration 					       TZSELECT(8)

NAME

       tzselect - select a timezone

SYNOPSIS

       tzselect

DESCRIPTION

       The  tzselect  program asks the user for information about the current location, and outputs the resulting timezone description to standard
       output.	The output is suitable as a value for the TZ environment variable.

       All interaction with the user is done via standard input and standard error.

EXIT STATUS

       The exit status is zero if a timezone was successfully obtained from the user, nonzero otherwise.

ENVIRONMENT

       AWK    Name of a Posix-compliant awk program (default: awk).

       TZDIR  Name of the directory containing timezone data files (default: /usr/share/zoneinfo).

FILES

       TZDIR/iso3166.tab
	      Table of ISO 3166 2-letter country codes and country names.

       TZDIR/zone.tab
	      Table of country codes, latitude and longitude, TZ values, and descriptive comments.

       TZDIR/TZ
	      Time zone data file for timezone TZ.

SEE ALSO

       tzfile(5), zdump(8), zic(8)

COLOPHON

       This page is part of release 3.55 of the Linux man-pages project.  A description of the project, and information about reporting bugs,  can
       be found at http://www.kernel.org/doc/man-pages/.

								    2007-05-18							       TZSELECT(8)

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