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Full Discussion: Clipping -awk
Top Forums UNIX for Dummies Questions & Answers Clipping -awk Post 302948825 by Xterra on Thursday 2nd of July 2015 06:38:01 PM
Old 07-02-2015
Clipping -awk
I have this infile:
Code:
>Sample23
acagtagaca-atagacgatggagagacatgaggcccaaaattt
>Sample-123
--agtagacagatagacgatggagagacatgaggcccaattt--
>Sample23 Freq 45
acagtagacagatagacgat-gagagacatgaggcccaaaattt
>Reference
---------agatagacgatggagagacatgaggccca------
>Sample__23
acagtagacagatagacgatggagagacatgaggcccaaaa---

I need to trim all sequences based on the Reference entry. This is the desire outfile:
Code:
>Sample23
a-atagacgatggagagacatgaggccca
>Sample-123
agatagacgatggagagacatgaggccca
>Sample23 Freq 45
agatagacgat-gagagacatgaggccca
>Reference
agatagacgatggagagacatgaggccca
>Sample__23
agatagacgatggagagacatgaggccca

I am able to trim the right side but not the left
Script
Code:
awk 'NR==FNR{if($0 ~ /Reference/){getline; gsub("-","");x=length;}next;}{print substr($0,1,x);}' infile infile

I would like to modify this script so I can understand what I am doing wrong
Thanks!
 

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LEARN ABOUT MOJAVE

locale::codes::langext5.18

Locale::Codes::LangExt(3pm)				 Perl Programmers Reference Guide			       Locale::Codes::LangExt(3pm)

NAME

       Locale::Codes::LangExt - standard codes for language extension identification

SYNOPSIS

	  use Locale::Codes::LangExt;

	  $lext = code2langext('acm');		       # $lext gets 'Mesopotamian Arabic'
	  $code = langext2code('Mesopotamian Arabic'); # $code gets 'acm'

	  @codes   = all_langext_codes();
	  @names   = all_langext_names();

DESCRIPTION

       The "Locale::Codes::LangExt" module provides access to standard codes used for identifying language extensions, such as those as defined in
       the IANA language registry.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default IANA language
       registry codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying language extensions. A code set may be specified using either a name, or
       a constant that is automatically exported by this module.

       For example, the two are equivalent:

	  $lext = code2langext('acm','alpha');
	  $lext = code2langext('acm',LOCALE_LANGEXT_ALPHA);

       The codesets currently supported are:

       alpha
	   This is the set of three-letter (lowercase) codes from the IANA language registry, such as 'acm' for Mesopotamian Arabic.

	   This is the default code set.

ROUTINES

       code2langext ( CODE [,CODESET] )
       langext2code ( NAME [,CODESET] )
       langext_code2code ( CODE ,CODESET ,CODESET2 )
       all_langext_codes ( [CODESET] )
       all_langext_names ( [CODESET] )
       Locale::Codes::LangExt::rename_langext  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangExt::add_langext  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangExt::delete_langext  ( CODE [,CODESET] )
       Locale::Codes::LangExt::add_langext_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangExt::delete_langext_alias  ( NAME )
       Locale::Codes::LangExt::rename_langext_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangExt::add_langext_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangExt::delete_langext_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes::API man page.

SEE ALSO

       Locale::Codes
	   The Locale-Codes distribution.

       Locale::Codes::API
	   The list of functions supported by this module.

       http://www.iana.org/assignments/language-subtag-registry
	   The IANA language subtag registry.

AUTHOR

       See Locale::Codes for full author history.

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

COPYRIGHT

	  Copyright (c) 2011-2013 Sullivan Beck

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

perl v5.18.2							    2013-11-04					       Locale::Codes::LangExt(3pm)
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