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Full Discussion: Array V-Lookup using UNIX bash
Top Forums Shell Programming and Scripting Array V-Lookup using UNIX bash Post 303016586 by Geneanalyst on Sunday 29th of April 2018 11:14:07 PM
Old 04-30-2018
RudyC,


Would the following modification to your script be adequate if the input file IN1 was like this instead:

Code:
awk 'NR == FNR {REP[$1] = $4; next} $1 in REP && FNR > 1 { $4 = REP[$1]; CNT++} 1; END {print CNT}' OFS="\t"

Code:
rsid    chromosome    position    alleles
rs4471    1    82154    TT
rs313    1    752721    GG
rs125    1    768448    GG
rs112    1    798959    GG
rs668    1    800007    CC
rs497    1    838555    AA
rs447    1    846808    TC
rs753    1    854250    AG
rs1330    1    861808    GG
rs111    1    873558    TG
rs171    1    887162    TT

And the desired output OUT needed to be :

Code:
rsid    chromosome    position    alleles
rs4471    1    82154    AA
rs313    1    752721    GG
rs125    1    768448    AG
rs112    1    798959    GG
rs668    1    800007    CC
rs497    1    838555    CC
rs447    1    846808    TC
rs753    1    854250    AG
rs1330    1    861808    AA
rs111    1    873558    TG
rs171    1    887162    TT

Last edited by Geneanalyst; 04-30-2018 at 12:37 AM..
 

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LEARN ABOUT OSX

locale::codes::langext

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) 2011-2012 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::LangExt(3pm)
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