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Full Discussion: awk script
Top Forums Shell Programming and Scripting awk script Post 302936745 by genebuster on Friday 27th of February 2015 10:43:54 AM
Old 02-27-2015
Quote:
Originally Posted by genebuster
Hi,
The input files are attached
---------- Post updated at 10:43 AM ---------- Previous update was at 10:42 AM ----------

Hi,

I am trying to find out overlapping regions in two given files, so I wrote a awk script
Code:
 awk 'FNR==NR {a[$1]; next} $1 in a'

My first input file is arranged like this:
Code:
 
chr7 751143 766356
chr7 825291 826114
chr7 826118 857092
chr7 912969 916281
chr7 935060 938556
chr7 995044 1009012
chr7 1015146 1022846
chr7 1028459 1037259

and the second input file like this:
Code:
 
chr1 10001 10468 (CCCTAA)n Simple_repeat
chr1 10469 11447 TAR1 Satellite/telo
chr1 11505 11675 L1MC5a LINE/L1
chr1 11678 11780 MER5B DNA/hAT-Charlie
chr1 15265 15355 MIR3 SINE/MIR
chr1 16713 16749 (TGG)n Simple_repeat
chr1 18907 19048 L2a LINE/L2
chr1 19972 20405 L3 LINE/CR1
chr1 20531 20679 Plat_L3 LINE/CR1

If I want to find out the overlapping regions between the two files having an output like this which contains elements from the first and the second file :
Code:
chr7 751143 766356 chr7 751143 766356 MIR3 SINE/MIR

How should I write the script ?
The output is just an example I have given to illustrate the overlaps between two files

Last edited by Scrutinizer; 02-27-2015 at 11:47 AM.. Reason: code tags
 

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IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME
igawk - gawk with include files SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ... igawk [ all gawk options ] [ -- ] program-text file ... DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1). AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like @include getopt.awk in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path. OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports. EXAMPLES
cat << EOF > test.awk @include getopt.awk BEGIN { while (getopt(ARGC, ARGV, "am:q") != -1) ... } EOF igawk -f test.awk SEE ALSO
gawk(1) Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995. AUTHOR
Arnold Robbins (arnold@skeeve.com). Free Software Foundation Nov 3 1999 IGAWK(1)
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