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Full Discussion: extract data from 2 files
Top Forums Shell Programming and Scripting extract data from 2 files Post 302597502 by Diya123 on Friday 10th of February 2012 01:19:52 PM
Old 02-10-2012
extract data from 2 files
file 1
Code:
WASH7P        17232,18267,18500,20564            17368,18362,18554,21139

file 2


Code:
chr1	14969	15038	Exon	WASH7P
chr1	17232	17368	Exon	WASH7P
chr1	17258	17368	Exon	WASH7P
chr1	17605	17742	Exon	WASH7P
chr1	18267	18362	Exon	WASH7P
chr1	18267	18366	Exon	WASH7P
chr1	18267	18369	Exon	WASH7P
chr1	18267	18379	Exon	WASH7P
chr1	18496	18554	Exon	WASH7P
chr1	18500	18554	Exon	WASH7P
chr1	18912	19139	Exon	WASH7P

What I need to check is for each gene if column 2 of file 2 is present in column 2 of file 1 and column 3 of file 2 is present in column 3 of file 1 . If so then these two are supposed to be placed in column 4 and 5 of file 1. I just explained one example here. I have 15000 entries with different genes(column5 of file 2). so a for loop should be there to iterate..

o/p

Code:
 WASH7P        17232,18267,18500,20564            17368,18362,18554,21139  17232,18267,18500   17232,18267,18500

Thanks,
Last edited by Franklin52; 02-11-2012 at 08:59 AM.. Reason: Adding code tags
 

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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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