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Full Discussion: Filtering my major and minor values
Top Forums Shell Programming and Scripting Filtering my major and minor values Post 302751881 by newbie83 on Friday 4th of January 2013 05:02:28 PM
Old 01-04-2013
Hi,

There is one more filter that needs to be considered.
I want to treat any character other than A,C,G,T,N as a missing value N.
In the example, the character Y is treated as if it was a missing value N since it
does not belong to the subset {A,C,G,T,N}.

For example the row
Code:
S10_14113072        A    C    C    A    A    Y

needs to be treated the same as
Code:
S10_14113072        A    C    C    A    A    N

But if such a row appears in the output it should appear as
Code:
S10_14113072        A    C    C    A    A    Y

---------- Post updated at 06:02 PM ---------- Previous update was at 05:57 PM ----------

I have done a small modification
Code:
if ($i != "[ACGTN]") { $i = "N" }

Doesnt seem to work. please help me with the correct code?


Code:
function initVars()
{
  split("",n)
  split("",a)
  c=0
}

{
  for(i=2;i<=NF;i++)
    if ($i != "[ACGTN]") { $i = "N" } 
    if ($i != "N") {
     if (!($i in a))
       n[++c]=$i
     a[$i]++
    }

  if (c>2) { initVars(); print;next }

  div=a[n[1]]/a[n[2]]
  div=(div>1)?1/div:div
  if ( div*100 > 30)
     print
  initVars()
}

Last edited by newbie83; 01-04-2013 at 06:18 PM..
 

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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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