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Full Discussion: Deleting sequences based on character frequency
Top Forums Shell Programming and Scripting Deleting sequences based on character frequency Post 302430293 by Xterra on Thursday 17th of June 2010 05:13:46 AM
Old 06-17-2010
A problem
If we use File A.fas contain the following sequences
Quote:
> Seq1 Freq 1
ATC
> Seq2 Freq 33
ACG
> Seq3 Freq 33
TTG
> Seq4 Freq 33
TCC
ANd then used your code
Code:
awk '/^>/{p=($5>=5)?1:0}p' A.fas > Unique.fas

As result I get Seq2, 3 and 4 but not Seq1. Now, if we determine the frequency of each character in Seq1, the values are always higher than 5% (34%), therefore it should also be kept. Thus, the code is not calculating the frequency of each character in each position (column) to decide whether to keep or remove the sequence. It is only considering the prevalence, if higher than 5% then the sequence will be kept.
I have also tried your last code:
Code:
$ awk '/^>/{id=$0;next}length>=5&&length<=18{F[$1]++;if (!I[$1]) I[$1]=id}END {for(i in I)printf "%s Freq %s\n%s\n",I[i],F[i],i}' A.fas > Unique.fas

But the Unique.fas file is empty.
Last edited by Xterra; 06-17-2010 at 06:22 AM..
 

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LEARN ABOUT MOJAVE

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) 2011-2013 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::LangFam(3pm)
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