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Search strings and highlight them using Perl or bash/awk/sed

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Top Forums Shell Programming and Scripting Search strings and highlight them using Perl or bash/awk/sed
# 8  
Old 08-11-2013
s#%#%&E#&%!!!

There was space after code in b.txt
Since I just copied it from post #1, I did not check.

Code:
cat -ev b.txt
GACAAGT $
AAAAAG $
TAATG$
CAAGC$
ACG $
GCTTG$

Now both awk and perl works fine.
Thanks.

Code:
awk 'NR==FNR {a[$0]=$0;next} {for (i in a) {gsub(a[i],"\033[1;31m&\033[0m",$0)}}1' b.txt a.txt
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49

This User Gave Thanks to Jotne For This Post:
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# 9  
Old 08-12-2013
Thanks bartus and Jotne. Smilie
Can you please explain the code.

Thanks.
# 10  
Old 08-12-2013
Code:
awk '	NR==FNR {a[$0]=$0;next}
 	{for (i in a) 
		{gsub(a[i],"\033[1;31m&\033[0m",$0)}
	}1
	' b.txt a.txt

NR==FNR {a[$0]=$0;next}
NR==FNR This is a technique used to do something on the first file, when more file are listed, in this case b.txt
a[$0]=$0 Store every record of b.txt in an array named a eks a[GACAAGT]=GACAAGT
for (i in a) for every element in array a (b.txt), test it against a.txt
gsub(a[i],"\033[1;31m&\033[0m",$0) Test every element in array a, against the line $0 from a.txt, if found replace the found text with itself & plus ansi color code.
Eks if found AGC, replace it with \033[1;31mAGC\033[0m = AGC
Then the 1 at the final will print all lines from a.txt with modified colors for every find.



Edit: the $0 at the final is not needed, since this is the default line to test
Also changing that array name to b, to reflect its store content of b.txt to make it more clear.
Code:
awk 'NR==FNR {b[$0]=$0;next} {for (i in b) {gsub(b[i],"\033[1;31m&\033[0m")}}1' b.txt a.txt



Edit2: no need to have b.txt stored as both value and index of array b
Code:
awk 'NR==FNR {b[$0]++;next} {for (i in b) {gsub(i,"\033[1;31m&\033[0m")}}1' b.txt a.txt

Last edited by Jotne; 08-12-2013 at 03:34 AM..
This User Gave Thanks to Jotne For This Post:
bioinfo
# 11  
Old 08-12-2013
Thanks a lot. Smilie
I will try them.
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