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Top Forums UNIX for Dummies Questions & Answers Loop with Perl (string search) Post 302969452 by Scrutinizer on Tuesday 22nd of March 2016 11:34:05 PM
Old 03-23-2016
Quote:
Originally Posted by rdrtx1
try:
Code:
#!/bin/bash
Primers=( NULL 'JOHN' )
for y in {1..1}
do
        perl -ple '/'${Primers[$y]}'/ and y/ACGT/TGCA/ and $_ = reverse unless /^>/' test.txt
done

Note that by doing this anything that is in ${Primers[$y]} will be unprotected by quotes from the shell and will be subject to field splitting an globbing..

To illustrate (in an empty directory):
Code:
$ touch foo bar
$ var="a   b*"
$ echo "$var"
a   b*
$ echo ''$var''
a bar


Last edited by Scrutinizer; 03-23-2016 at 12:42 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 filename 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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