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 OSF1

ppmtopgm

ppmtopgm(1)						      General Commands Manual						       ppmtopgm(1)

NAME

       ppmtopgm - convert a portable pixmap into a portable graymap

SYNOPSIS

       ppmtopgm [ppmfile]

DESCRIPTION

       Reads  a  portable  pixmap  as  input.  Produces a portable graymap as output.  The output is a "black and white" rendering of the original
       image, as in a black and white photograph.  The quantization formula used is .299 r + .587 g + .114 b.

       Note that although there is a pgmtoppm program, it is not necessary for simple conversions from pgm to ppm , because any  ppm  program  can
       read  pgm  (and	pbm  ) files automatically.  pgmtoppm is for colorizing a pgm file.  Also, see ppmtorgb3 for a different way of converting
       color to gray.  And ppmdist generates a grayscale image from a color image, but in a way that makes it easy to differentiate  the  original
       colors, not necessarily a way that looks like a black and white photograph.

QUOTE

       Cold-hearted orb that rules the night
       Removes the colors from our sight
       Red is gray, and yellow white
       But we decide which is right
       And which is a quantization error.

SEE ALSO

       pgmtoppm(1),ppmtorgb3(1),rgb3toppm(1),ppmdist(1),ppm(5),pgm(5)

AUTHOR

       Copyright (C) 1989 by Jef Poskanzer.

								   10 April 2000						       ppmtopgm(1)

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