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Top Forums Shell Programming and Scripting Search strings and highlight them using Perl or bash/awk/sed Post 302842915 by Jotne on Sunday 11th of August 2013 08:01:32 AM
Old 08-11-2013
@bartus11
Here is what I got when run your code
Code:
perl -lpe 'BEGIN{open b, "b.txt";chomp(@b=<b>)}{for $i (@b) {s/$i/\033[31m$i\033[0m/g}}' a.txt
Seq1 -------------------------------TTAAAAAGTTTGAGTTCTAAA---------------- 21
Seq2 -----CTTGGCTCTTTCGTAAGTTTTTCATTAAGGAACTTGAATACACGGTTT----AC- 50
Seq3 TTAAACTTTTTTCAACCCTAATG-----CGGTTTGAACCATTAACC-----------TAAC 48
Seq4 --------GAAAGGAGCGGAGTG-GTCACGTGACAAGTTCTCAGACGCACGTGC--TTGT 49

As you see, it show the line with hits, but only highlight one hit, look at my post #4.
OP request is color on all data in bold.


For some strange reason this has same problem, it only highlight one hits.
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


Last edited by Jotne; 08-11-2013 at 09:36 AM..
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RBASH(1)						      General Commands Manual							  RBASH(1)

NAME
rbash - restricted bash, see bash(1) RESTRICTED SHELL
If bash is started with the name rbash, or the -r option is supplied at invocation, the shell becomes restricted. A restricted shell is used to set up an environment more controlled than the standard shell. It behaves identically to bash with the exception that the follow- ing are disallowed or not performed: o changing directories with cd o setting or unsetting the values of SHELL, PATH, ENV, or BASH_ENV o specifying command names containing / o specifying a file name containing a / as an argument to the . builtin command o specifying a filename containing a slash as an argument to the -p option to the hash builtin command o importing function definitions from the shell environment at startup o parsing the value of SHELLOPTS from the shell environment at startup o redirecting output using the >, >|, <>, >&, &>, and >> redirection operators o using the exec builtin command to replace the shell with another command o adding or deleting builtin commands with the -f and -d options to the enable builtin command o using the enable builtin command to enable disabled shell builtins o specifying the -p option to the command builtin command o turning off restricted mode with set +r or set +o restricted. These restrictions are enforced after any startup files are read. When a command that is found to be a shell script is executed, rbash turns off any restrictions in the shell spawned to execute the script. SEE ALSO
bash(1) GNU Bash-4.0 2004 Apr 20 RBASH(1)
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