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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 CENTOS

paps

PAPS(1) 						      General Commands Manual							   PAPS(1)

NAME

       paps - UTF-8 to PostScript converter using Pango

SYNOPSIS

       paps [options] files...

DESCRIPTION

       paps reads a UTF-8 encoded file and generates a PostScript language rendering of the file. The rendering is done by creating outline curves
       through the pango ft2 backend.

OPTIONS

       These programs follow the usual GNU command line syntax, with long options starting with  two  dashes  (`-').   A  summary  of  options	is
       included below.

       --landscape
	      Landscape output. Default is portrait.

       --columns=cl
	      Number of columns output. Default is 1.

       --font=desc
	      Set the font description. Default is Monospace 12.

       --rtl  Do rtl layout.

       --paper ps
	      Choose paper size. Known paper sizes are legal, letter, a4. Default is A4.

       --bottom-margin=bm
	      Set bottom margin in postscript points (1/72 inch). Default is 36.

       --top-margin=tm
	      Set top margin. Default is 36.

       --left-margin=lm
	      Set left margin. Default is 36.

       --right-margin=rm
	      Set right margin. Default is 36.

       --help Show summary of options.

       --header
	      Draw page header for each page.

       --markup
	      Interpret the text as pango markup.

       --encoding=ENCODING
	      Assume the documentation encoding is ENCODING.

       --lpi  Set the lines per inch. This determines the line spacing.

       --cpi  Set the characters per inch. This is an alternative method of specifying the font size.

       --stretch-chars
	      Indicates  that  characters  should be stretched in the y-direction to fill up their vertical space. This is similar to the texttops
	      behaviour.

AUTHOR

       paps was written by Dov Grobgeld <dov.grobgeld@gmail.com>.

       This manual page was written by Lior Kaplan <kaplan@debian.org>, for the Debian project (but may be used by others).

								  April  17, 2006							   PAPS(1)
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