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Top Forums Shell Programming and Scripting File w/ many line pairs--how do I order based on 1st lines only? Post 302839899 by pathunkathunk on Saturday 3rd of August 2013 03:07:24 PM
File w/ many line pairs--how do I order based on 1st lines only?

I have a file in which the data is stored in pairs of lines. The first line (beginining with ">") is a header, the second line is a sequence.
Quote:
>gi|31425523|gb|AY987736.1|_Macrosiphum_rosae
TCCGTGGAGATGCACCACGAAGCT
>gi|512740870|gb|JX507490.1|_Macrosiphum_funestum
GTCGTGTAGAAA-CTGGTCTT
>gi|336390332|gb|HQ651228.1|_Cryptomyzus_maudamanti
GTTTTCGCACCAGCA
>gi|0|mcg|0|_Aulacorthum_albimagnoliae
A-GTCAGCAGTTAC
I would like to sort the file by species name. Desired output for the example file:
Quote:
>gi|0|mcg|0|_Aulacorthum_albimagnoliae
A-GTCAGCAGTTAC
>gi|336390332|gb|HQ651228.1|_Cryptomyzus_maudamanti
GTTTTCGCACCAGCA
>gi|512740870|gb|JX507490.1|_Macrosiphum_funestum
GTCGTGTAGAAA-CTGGTCTT
>gi|31425523|gb|AY987736.1|_Macrosiphum_rosae
TCCGTGGAGATGCACCACGAAGCT
I can use
Code:
sort -t'_' -k2

to alphabetize headers in the correct way, but I'm not sure how to bring the sequences (second lines of each pair) along for the ride. Can anyone help?
 
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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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