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Top Forums Shell Programming and Scripting Trimming sequences based on specific pattern Post 302432062 by Xterra on Wednesday 23rd of June 2010 06:36:26 PM
Old 06-23-2010
Trimming sequences based on specific pattern

My files look like this
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTACGCCCCGGGGC
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTACCCGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTAGATTTTCTGGGGCCCCGGGG
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTATAGCTGGATTTTCTGGGACGCCCCGGGGTGC
And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted.
Quote:
AGCCCTA
The expected result should look like this
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTA
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTA
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTA
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTA
Thus, all the sequences would end with AGCCCTA but whatever is to the left of that particular pattern and the identifiers (>GHXCZCC01AJ8CJ) should be kept intact.
Thanks in advance
 

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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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