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Full Discussion: Loop with Perl (string search)
Top Forums UNIX for Dummies Questions & Answers Loop with Perl (string search) Post 302969450 by Scrutinizer on Tuesday 22nd of March 2016 11:30:42 PM
Old 03-23-2016
The single quotes prevent the shell from expanding the shell array variable ${Primers[$y]}.
You can try:
Code:
perl -ple "/${Primers[$y]}/"' and y/ACGT/TGCA/ and $_ = reverse unless /^>/' test.txt

or pass the variable:
Code:
perl -sple '$_=~$match and y/ACGT/TGCA/ and $_ = reverse unless /^>/' -- -match="${Primers[$y]}"

--
Note that repeatedly calling an external program, like awk or perl from inside a shell loop is less efficient and detrimental to performance. It could be done more efficiently by looping inside these programs themselves...
 

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LEARN ABOUT MOJAVE

set_color

set_color(1)							       fish							      set_color(1)

NAME

       set_color - set_color - set the terminal color

set_color - set the terminal color
   Synopsis
       set_color [-v --version] [-h --help] [-b --background COLOR] [COLOR]

   Description
       Change the foreground and/or background color of the terminal. COLOR is one of black, red, green, brown, yellow, blue, magenta, purple,
       cyan, white and normal.

       o -b, --background Set the background color

       o -c, --print-colors Prints a list of all valid color names

       o -h, --help Display help message and exit

       o -o, --bold Set bold or extra bright mode

       o -u, --underline Set underlined mode

       o -v, --version Display version and exit

       Calling set_color normal will set the terminal color to whatever is the default color of the terminal.

       Some terminals use the --bold escape sequence to switch to a brighter color set. On such terminals, set_color white will result in a grey
       font color, while set_color --bold white will result in a white font color.

       Not all terminal emulators support all these features. This is not a bug in set_color but a missing feature in the terminal emulator.

       set_color uses the terminfo database to look up how to change terminal colors on whatever terminal is in use. Some systems have old and
       incomplete terminfo databases, and may lack color information for terminals that support it. Download and install the latest version of
       ncurses and recompile fish against it in order to fix this issue.

Version 1.23.1							  Sun Jan 8 2012						      set_color(1)
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