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Full Discussion: awk to match field4 and field5, field6 and field7, field8 and field9 and so on.
Top Forums Shell Programming and Scripting awk to match field4 and field5, field6 and field7, field8 and field9 and so on. Post 302955871 by huiyee1 on Wednesday 23rd of September 2015 01:34:23 AM
Old 09-23-2015
Hi disedorgue and RudiC,

I need to add in one more condition another input file as follows,
if field4≠field5 and field4≠NN and field5≠NN, print NN

Input2:
Code:
loc01	1000560	G	AA	AG	GC	GA	AC	AG	NN	NN	NN	NN
loc02	1001612	C	NN	NN	CT	CC	NN	NN	NN	NN	CT	NN
loc03	1001797	C	AC	NN	NN	NN	NN	NN	NN	NN	AC	NN
loc04	1004204	G	NN	AG	NN	NN	NN	NN	AG	NN	AG	NN
loc05	1005484	C	NN	NN	CT	NN	NN	NN	NN	NN	NN	NN
loc06	1005486	C	CT	CG	CT	NN	NN	NN	NN	NN	NN	NN
loc07	1005499	G	NN	NN	AG	NN	NN	NN	NN	NN	NN	NN
loc08	100707	T	NN	NN	NN	NN	NN	NN	NN	NN	NN	NN
loc09	100937	C	NN	NN	NN	NN	NN	NN	CT	NN	NN	NN
loc10	100949	C	NN	NN	NN	NN	NN	NN	CT	NN	NN	NN
loc11	101063	T	NN	NN	NN	NN	NN	CT	NN	NN	CT	NN
loc12	1010912	G	AG	AG	AG	NN	AG	NN	AG	NN	NN	AG
loc13	1011214	A	NN	NN	NN	AG	NN	NN	NN	NN	AG	AG
loc14	1011673	T	NN	CT	CT	NN	CT	NN	CT	NN	CT	CT
loc15	1011981	A	NN	NN	NN	NN	NN	AG	NN	NN	NN	NN
loc16	1012439	C	NN	NN	NN	NN	NN	NN	NN	NN	NN	CT
loc17	1012718	T	NN	NN	CT	NN	CT	NN	CT	NN	CT	NN
loc18	1015524	A	NN	NN	NN	NN	AT	AT	AT	NN	AT	NN
loc19	1023408	C	CG	NN	NN	NN	NN	CG	NN	NN	NN	NN
loc20	102483	A	AA	CC	CC	CT	NN	NN	NN	NN	NN	NN

Output2:
Code:
loc01	1000560	G	NN	NN	NN	NN	NN
loc02	1001612	C	NN	NN	NN	NN	CT
loc03	1001797	C	AC	NN	NN	NN	AC
loc04	1004204	G	AG	NN	NN	AG	AG
loc05	1005484	C	NN	CT	NN	NN	NN
loc06	1005486	C	NN	CT	NN	NN	NN
loc07	1005499	G	NN	AG	NN	NN	NN
loc08	100707	T	NN	NN	NN	NN	NN
loc09	100937	C	NN	NN	NN	CT	NN
loc10	100949	C	NN	NN	NN	CT	NN
loc11	101063	T	NN	NN	CT	NN	CT
loc12	1010912	G	AG	AG	AG	AG	AG
loc13	1011214	A	NN	AG	NN	NN	AG
loc14	1011673	T	CT	CT	CT	CT	CT
loc15	1011981	A	NN	NN	AG	NN	NN
loc16	1012439	C	NN	NN	NN	NN	CT
loc17	1012718	T	NN	CT	CT	CT	CT
loc18	1015524	A	NN	NN	AT	AT	AT
loc19	1023408	C	CG	NN	CG	NN	NN
loc20	102483	A	NN	NN	NN	NN	NN

I tried to use the following script modified from disedorgue, but i failed.
Code:
 awk '{
printf("%s\t%s\t%s\t",$1,$2,$3)
for(i=4;i<=NF;i+=2){
   if($i==$(i+1)) new=$i;
   else if($i=="NN" || $(i+1)!="NN") new=$(i+1);
   else if($i!="NN" || $(i+1)=="NN") new=$i;
   else if($i!=$(i+1) || $i!="NN" || $(i+1)!="NN") new=NN;
   printf("%s\t",new)} print ""}' input2.txt

What is the mistake I have made?

---------- Post updated 09-23-15 at 12:34 AM ---------- Previous update was 09-22-15 at 08:50 PM ----------

Hi all,

I figured it out using the following script:
Code:
awk '{
printf("%s\t%s\t%s\t",$1,$2,$3)
for(i=4;i<=NF;i+=2){
   if($i==$(i+1)) new=$i;
   else if($i=="NN" && $(i+1)!="NN") new=$(i+1);
   else if($i!="NN" && $(i+1)=="NN") new=$i; 
   else if($i!=$(i+1) && $i!="NN" && $(i+1)!="NN") new="NN";
   printf("%s\t",new)} print ""}' input2.txt

 

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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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