Search for string in column using variable: awk Post: 303012408

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Top Forums Shell Programming and Scripting Search for string in column using variable: awk Post 303012408 by genome on Saturday 3rd of February 2018 05:47:21 PM

02-03-2018

Registered User

Search for string in column using variable: awk

I'm interested to match column pattern through awk using an external variable for data:

Code:

-9	1:751343:T:A	-9	0	T	A	0.726	-5.408837e-03	9.576603e-03	7.967536e-01	5.722312e-01
-9	1:751756:T:C	-9	0	T	C	0.727	-5.360458e-03	9.579447e-03	7.966977e-01	5.757858e-01
-9	1:752566:G:A	-9	0	G	A	0.331	6.583382e-03	8.958503e-03	7.950995e-01	4.624419e-01
-9	1:753425:T:C	-9	0	T	C	0.295	7.321481e-03	
-9	3:60197:G:A	-9	0	G	A	0.918	1.480658e-03	1.554497e-02	7.950968e-01	9.241192e-01
-9	3:60202:C:G	-9	0	C	G	0.989	-2.318091e-02	2.707507e-02	7.947803e-01	5.699114e-01
-9	22:51228888:T:G	-9	0	T	G	0.737	-7.274594e-03	1.073497e-02	7.928675e-01	4.980153e-01
-9	22:51228910:G:A	-9	0	G	A	0.791	-6.978814e-03	1.147448e-02	7.936905e-01	5.430739e-01
-9	22:51229455:G:C	-9	0	G	C	0.965	4.726587e-03	2.609153e-02	7.949339e-01	8.562523e-01
-9	22:51229491:G:A	-9	0	G	A	0.970	5.992810e-02	2.711477e-02	7.917267e-01	2.712828e-02
-9	22:51229591:A:G	-9	0	A	G	0.988	1.235893e-01	4.360370e-02	7.923663e-01	4.605606e-03
-9	22:51229717:A:T	-9	0	A	T	0.791	-4.919975e-03	1.159186e-02	7.941657e-01	6.712634e-01

The data are stored in more.txt file.

Code:

for i in {1..22} 
do  

printf "$i\n" 

awk -v chr=$i '{

if ($2 ~ /^chr:/ )
{
print $0 
} 
}' more.txt

done

Issue:
The match pattern doesn't pick chr variable. It works fine if I put number (hard coded). It prints chr variable correctly though.

Only numbers through 1 to 22 are printed for the for loop.

Darwin 17.3.0 Darwin Kernel Version 17.3.0: Thu Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64
OSX 10.13.2

Last edited by genome; 02-03-2018 at 06:47 PM.. Reason: edited data

genome

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LEARN ABOUT LINUX

igawk

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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