Getting the non-homogenous letter row from a text file Post: 302818767

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Top Forums Shell Programming and Scripting Getting the non-homogenous letter row from a text file Post 302818767 by Lucky Ali on Sunday 9th of June 2013 09:30:09 AM

06-09-2013

Registered User

Alphabet counting

Thanks That worked.
I would like to get another awk solution. I have a file with the following format

Code:

CCCCCGCCCCCCCCCCcCCCCCCCCCCCCCCC
AAAATAAAAAAAAAAAaAAAAAAAAAAAAAAA
TGTTTTTTTTTTTTGGtTTTTTTTTTTTTTTT
TTTT-TTTTTTTTTCTtTTTTTTTTTTTTTTT

Each row/line will have 32 letters and each line will only have multiple occurrences of 2 or more letters out of a pool of ATGC (also small atgc). some may have also '-'. I would like to count the occurrence of each alphabet in a line and output the position number/ numbers of all the counted alphabet.

Desired output is

Code:

CCCCCGCCCCCCCCCCcCCCCCCCCCCCCCCC C 1 2 3 4 5 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 G 6
AAAATAAAAAAAAAAAaAAAAAAAAAAAAAAA A 1 2 3 4 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32   T 5
TGTTTTTTTTTTTTGGtTTTTTTTTTTTTTTT T 1 3 4 5 7 8 9 10 11 12 13 14 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32  G 2 15 16 
TTTT-TTTTTTTTTCTtTTTTTTTTTTTTTTT T 1 2 3 4 6 7 8 9 10 11 12 13 14 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 C 15

Please let me know the best way to do this in awk.

---------- Post updated at 09:30 AM ---------- Previous update was at 05:41 AM ----------

Is there a way to do it in either perl or awk??? looking forward to see suggestions

Lucky Ali

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LEARN ABOUT OSX

locale::codes::langfam

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

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) 2011-2012 Sullivan Beck

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

perl v5.16.2							    2012-10-11					       Locale::Codes::LangFam(3pm)