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Top Forums Shell Programming and Scripting Replacing headers based on a second file Post 302542759 by Xterra on Thursday 28th of July 2011 01:19:26 PM
Old 07-28-2011
Replacing headers based on a second file

I have a file with thousands of sequences that looks like this:
Quote:
>SeqID1
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
>Sequence 22
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
>Seq-39
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
I need to replace the headers using a second file
Quote:
HIV
WNV
Flu
Thus, I will end up having the following file:
Quote:
>HIV
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
>WNV
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
>Flu
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
I am looking for an AWK script that I can easily plug in my current pipeline.
Any help will be greatly appreciated!
 

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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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