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Full Discussion: Loop with Perl (string search)
Top Forums UNIX for Dummies Questions & Answers Loop with Perl (string search) Post 302969447 by Xterra on Tuesday 22nd of March 2016 10:56:38 PM
Old 03-22-2016
Loop with Perl (string search)
I am using a perl script to reverse and complement sequences if a string is found. The script works as expected as standalone but I would like to use it in my bash file. However, I am not getting my expected result.
My test.txt file
Code:
>Sample_72
CCCCTCGCGACCTGGATGTGTCGGCGTTTGTCATGTTTTCGTCGATGGCCGGGCTGGTCGGATCGTCSREVERGGGCCAGGCCAAAA
>Sample_2
CCCCTCGCGAJOHNCCTGGATGTGTCGGCGTTTGTCATGTTTTCGTCGATGGCCGGGCTGGTCGGATCGTCSREVERGGGCCAGGCCAAAA

Standalone Perl script:
Code:
perl -ple '/JOHN/ and y/ACGT/TGCA/ and $_ = reverse unless /^>/' test.txt

I get the expected output:
Code:
>Sample_72
CCCCTCGCGACCTGGATGTGTCGGCGTTTGTCATGTTTTCGTCGATGGCCGGGCTGGTCGGATCGTCSREVERGGGCCAGGCCAAAA
>Sample_2
TTTTGGCCTGGCCCREVERSGACGATCCGACCAGCCCGGCCATCGACGAAAACATGACAAACGCCGACACATCCAGGNHOJTCGCGAGGGG

Bash file:
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

Unexpected output:
Code:
>Sample_72
TTTTGGCCTGGCCCREVERSGACGATCCGACCAGCCCGGCCATCGACGAAAACATGACAAACGCCGACACATCCAGGTCGCGAGGGG
>Sample_2
TTTTGGCCTGGCCCREVERSGACGATCCGACCAGCCCGGCCATCGACGAAAACATGACAAACGCCGACACATCCAGGNHOJTCGCGAGGGG

in the bash file, the script reverses and complements the sequences regardless of the presence or absence of the string (JOHN)
I guess I still do not understand the proper use of slashes
 

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LEARN ABOUT DEBIAN

locale::script

Locale::Script(3perl)					 Perl Programmers Reference Guide				     Locale::Script(3perl)

NAME

       Locale::Script - standard codes for script identification

SYNOPSIS

	  use Locale::Script;

	  $script  = code2script('phnx');		      # 'Phoenician'
	  $code    = script2code('Phoenician'); 	      # 'Phnx'
	  $code    = script2code('Phoenician',
				 LOCALE_CODE_NUMERIC);	      # 115

	  @codes   = all_script_codes();
	  @scripts = all_script_names();

DESCRIPTION

       The "Locale::Script" module provides access to standards codes used for identifying scripts, such as those defined in ISO 15924.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 15924
       four-letter codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying scripts. The ones currently supported are:

       alpha
	   This is a set of four-letter (capitalized) codes from ISO 15924 such as 'Phnx' for Phoenician.

	   This code set is identified with the symbol "LOCALE_SCRIPT_ALPHA".

	   The Zxxx, Zyyy, and Zzzz codes are not used.

	   This is the default code set.

       numeric
	   This is a set of three-digit numeric codes from ISO 15924 such as 115 for Phoenician.

	   This code set is identified with the symbol "LOCALE_SCRIPT_NUMERIC".

ROUTINES

       code2script ( CODE [,CODESET] )
       script2code ( NAME [,CODESET] )
       script_code2code ( CODE ,CODESET ,CODESET2 )
       all_script_codes ( [CODESET] )
       all_script_names ( [CODESET] )
       Locale::Script::rename_script  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Script::add_script  ( CODE ,NAME [,CODESET] )
       Locale::Script::delete_script  ( CODE [,CODESET] )
       Locale::Script::add_script_alias  ( NAME ,NEW_NAME )
       Locale::Script::delete_script_alias  ( NAME )
       Locale::Script::rename_script_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Script::add_script_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Script::delete_script_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes man page.

SEE ALSO

       Locale::Codes
       Locale::Constants
       http://www.unicode.org/iso15924/
	   Home page for ISO 15924.

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 1997-2001 Canon Research Centre Europe (CRE).
	  Copyright (c) 2001-2010 Neil Bowers
	  Copyright (c) 2010-2011 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.14.2							    2011-09-26						     Locale::Script(3perl)
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