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Full Discussion: trimming sequences
Top Forums Shell Programming and Scripting trimming sequences Post 302431727 by Xterra on Tuesday 22nd of June 2010 06:48:45 PM
Old 06-22-2010
trimming sequences

My file looks like this:
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGC
CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCC
CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACG
CCCCGGGG
But I would like to 'trim' all sequences to the same lenght 32 characters, keeping intact all the identifier (>GHXCZCC01AJ8CJ)
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAG
CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGC
CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCA
CCCCGGGG
Would it be possible to use awk to perform this task?
 

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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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