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Full Discussion: awk to filter file using another working on smaller subset
Top Forums Shell Programming and Scripting awk to filter file using another working on smaller subset Post 302986976 by RavinderSingh13 on Friday 2nd of December 2016 11:21:41 PM
Old 12-03-2016
Quote:
Originally Posted by cmccabe
What would you recommend? The awk seems to work as expected with a limited data set. There are many lines that are similar in that they have ; separating but the name will be in there.
Thank you Smilie
Hello cmccabe,

Not sure if this is the required output you need by seeing your try only I have made it, could you please try following and let me know if this helps you.
Code:
awk -F"\t" 'FNR==NR{A[$0];next} {split($8, B,";");P=B[1]} (P in A){$1=++c;print}' gene file

Output will be as follows.
Code:
1 chr18 53303101 53303101 C G intergenic TCF4;ST8SIA3 dist=47241;dist=1716620 . . . rs611326 1. 1. 0.99 1. 1. 1. 1. 1. 0.99 1. 1. 1. 1. 1. 1. 1. 1. 1. 0.99 . . 1 T . B . B . . 1.000 P . . . . . . . GOOD 80 hom 23 . .

You could set output field seprator as TAB in case you need it.

NOTE: You haven't splited 8th field in Input_file named file so only it can't find it in the array which is being created during first file reading.

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
 

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LEARN ABOUT MOJAVE

locale::codes::langvar

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

NAME

       Locale::Codes::LangVar - standard codes for language variation identification

SYNOPSIS

	  use Locale::Codes::LangVar;

	  $lvar = code2langvar('acm');		       # $lvar gets 'Mesopotamian Arabic'
	  $code = langvar2code('Mesopotamian Arabic'); # $code gets 'acm'

	  @codes   = all_langvar_codes();
	  @names   = all_langvar_names();

DESCRIPTION

       The "Locale::Codes::LangVar" module provides access to standard codes used for identifying language variations, 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 variations. 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:

	  $lvar = code2langvar('en','alpha-2');
	  $lvar = code2langvar('en',LOCALE_CODE_ALPHA_2);

       The codesets currently supported are:

       alpha
	   This is the set of alphanumeric codes from the IANA language registry, such as 'arevela' for Eastern Armenian.

	   This code set is identified with the symbol "LOCALE_LANGVAR_ALPHA".

	   This is the default code set.

ROUTINES

       code2langvar ( CODE [,CODESET] )
       langvar2code ( NAME [,CODESET] )
       langvar_code2code ( CODE ,CODESET ,CODESET2 )
       all_langvar_codes ( [CODESET] )
       all_langvar_names ( [CODESET] )
       Locale::Codes::LangVar::rename_langvar  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangVar::add_langvar  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangVar::delete_langvar  ( CODE [,CODESET] )
       Locale::Codes::LangVar::add_langvar_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangVar::delete_langvar_alias  ( NAME )
       Locale::Codes::LangVar::rename_langvar_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangVar::add_langvar_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangVar::delete_langvar_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) 2011-2013 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							    2014-01-06					       Locale::Codes::LangVar(3pm)
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