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Full Discussion: Matching two files with special field separator
Top Forums Shell Programming and Scripting Matching two files with special field separator Post 302878844 by zozoo on Monday 9th of December 2013 08:02:48 AM
Old 12-09-2013
Quote:
Originally Posted by Homa
Hello,

I have a file with such structure:

Code:
>ENSGALG00000000011|ENSGALT00000000012|57|1123|1125
AACTGTGTGTTTTTT
>ENSGALG00000000012|ENSGALT00000000013|57|1145|1155
AAAAAAGGTCCTGTGTGC
>ENSGALG00000000015|ENSGALT00000000014|57|1144|1155
AAAATGTGTGTGTGTGTGTGTG

I want to use another file to extract the ones that have a specific idea in the first part, that is to use this file:

Code:
ENSGALG00000000011
ENSGALG00000000015

To get the final output like this:

Code:
>ENSGALG00000000011|ENSGALT00000000012|57|1123|1125
AACTGTGTGTTTTTT
>ENSGALG00000000015|ENSGALT00000000014|57|1144|1155
AAAATGTGTGTGTGTGTGTGTG

I know this code:

Code:
awk 'FNR == NR {_[$1]++} FNR < NR {if ( $1 in _ ) print $1, $0}' filetwo fileone

to compare the first fields of two files and print the matched ones but because of this special field separators, I don't know how this is feasible with this example.

Thanks a lot in advance for your help.
Cheers,


i think you can give a try with
Code:
awk -F

option to specify the filed limiter of your choice.
This User Gave Thanks to zozoo For This Post:
Homa
 

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LEARN ABOUT OSX

ppmtosixel

ppmtosixel(1)						      General Commands Manual						     ppmtosixel(1)

NAME

       ppmtosixel - convert a portable pixmap into DEC sixel format

SYNOPSIS

       ppmtosixel [-raw] [-margin] [ppmfile]

DESCRIPTION

       Reads  a  portable  pixmap  as input.  Produces sixel commands (SIX) as output.	The output is formatted for color printing, e.g. for a DEC
       LJ250 color inkjet printer.

       If RGB values from the PPM file do not have maxval=100, the RGB values are rescaled.  A printer control header and a color assignment table
       begin the SIX file.  Image data is written in a compressed format by default.  A printer control footer ends the image file.

OPTIONS

       -raw   If  specified,  each  pixel  will  be explicitly described in the image file.  If -raw is not specified, output will default to com-
	      pressed format in which identical adjacent pixels are replaced by "repeat pixel" commands.  A raw file is often an order	of  magni-
	      tude larger than a compressed file and prints much slower.

       -margin
	      If  -margin  is not specified, the image will be start at the left margin (of the window, paper, or whatever).  If -margin is speci-
	      fied, a 1.5 inch left margin will offset the image.

PRINTING

       Generally, sixel files must reach the printer unfiltered.  Use the lpr -x option or cat filename > /dev/tty0?.

BUGS

       Upon rescaling, truncation of the least significant bits of RGB values may result in poor color conversion.  If the original PPM maxval was
       greater	than  100,  rescaling  also reduces the image depth.  While the actual RGB values from the ppm file are more or less retained, the
       color palette of the LJ250 may not match the colors on your screen.  This seems to be a printer limitation.

SEE ALSO

       ppm(5)

AUTHOR

       Copyright (C) 1991 by Rick Vinci.

								   26 April 1991						     ppmtosixel(1)
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