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Full Discussion: Reporting characters after string
Top Forums UNIX for Dummies Questions & Answers Reporting characters after string Post 302970651 by Xterra on Sunday 10th of April 2016 01:46:01 AM
Old 04-10-2016
Reporting characters after string
I have a file that looks like this:
Code:
>ID 1
AATAATTCCGGATCGTGC
>ID 2
TTTGACAGTAGAC
>ID 3
AGACGATGACGAT

I am using the following script to report if AATTCCGGATCG is present in any sequence:
Code:
awk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} { print n "\t" (/AATTCCGGATCG|CGATCCGGAATT/ ? "ATCG" : "NOT Present" ) }

However, what I really need is the four characters right after the given string (AATTCCGG), in my example=ATCG. Importantly, the string can be found reversed GGCCTTAA and complemented A=T; T=A; C=G and G=C, originating the following string =CCGGAATT in the sequence. If the string is found reversed and complemented, the four characters after the string must be reported as reversed and complemented. Thus, the desired output from a file containing the following sequences:
Code:
>ID 1
AATAATTTTGGATCGTGC
>ID 2
TTTGACGTTCCGGAATTCAGTAGAC
>ID 3
AGACGATGACGAT

would be AACG, since sequence 2 contains the corresponding string, only reversed and complemented.
My script can deal with the fact that the sequence is reversed/complemented. However, if any of the positions after the string is mutated, it will not detect it. That's is why I would rather get the characters instead
Any help will be greatly appreciated
Thanks
PS. The string, in this case AATTCCGG or CCGGAATT will never be mutated in a real scenario.
 

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LEARN ABOUT CENTOS

locale::codes::langfam

Locale::Codes::LangFam(3)				User Contributed Perl Documentation				 Locale::Codes::LangFam(3)

NAME

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

SYNOPSIS

	  use Locale::Codes::LangFam;

	  $lext = code2langfam('apa');		       # $lext gets 'Apache languages'
	  $code = langfam2code('Apache languages');    # $code gets 'apa'

	  @codes   = all_langfam_codes();
	  @names   = all_langfam_names();

DESCRIPTION

       The "Locale::Codes::LangFam" module provides access to standard codes used for identifying language families, such as those as defined in
       ISO 639-5.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 639-5
       language family codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying language families. 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 = code2langfam('apa','alpha');
	  $lext = code2langfam('apa',LOCALE_LANGFAM_ALPHA);

       The codesets currently supported are:

       alpha
	   This is the set of three-letter (lowercase) codes from ISO 639-5 such as 'apa' for Apache languages.

	   This is the default code set.

ROUTINES

       code2langfam ( CODE [,CODESET] )
       langfam2code ( NAME [,CODESET] )
       langfam_code2code ( CODE ,CODESET ,CODESET2 )
       all_langfam_codes ( [CODESET] )
       all_langfam_names ( [CODESET] )
       Locale::Codes::LangFam::rename_langfam  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangFam::add_langfam  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangFam::delete_langfam  ( CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangFam::delete_langfam_alias  ( NAME )
       Locale::Codes::LangFam::rename_langfam_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::delete_langfam_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.loc.gov/standards/iso639-5/id.php
	   ISO 639-5 .

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 v5.16.3							    2013-02-27						 Locale::Codes::LangFam(3)
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