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Full Discussion: Help with processing coordinates in a file.
Top Forums UNIX for Beginners Questions & Answers Help with processing coordinates in a file. Post 303030112 by RudiC on Wednesday 6th of February 2019 05:58:44 AM
Old 02-06-2019
Please explain how this line
Code:
Solyc00g005060.1.1    SL3.0ch02    702679    C    A    -    -    -    -    -    -    -    -

made it into the desired ouput - there is no connection between Solyc00g005060.1.1 and SL3.0ch02 in your annotation file, but it exists for the Solyc00g005000.3.1 and SL3.0ch02 pair. And, why isn't Solyc00g005050.3.1 / SL3.0ch00 mentioned? Shouldn't that match the third variation line?


Howsoever, pls try and report back
Code:
awk '
NR==FNR         {a[$2 FS $3 FS $4] = $1
                 next
                }
                {for (i in a) if (split (i,t) && $2>=t[2] && $2<=t[3])  print a[i], $0
                }
' annotation.txt variation.txt
Solyc00g005000.3.1 SL3.0ch02     702679    C     A     -     -     -     -     -     -     -     -    
Solyc00g005040.3.1 SL3.0ch00     715124    G     A     -     -     -     -     -     -     -     -
Solyc00g005060.1.1 SL3.0ch00     723860    A     C     Solyc00g005060.1     CDS     NONSYNONYMOUS     W/G     52    0    novel     DELETERIOUS (*WARNING! Low confidence)
Solyc00g005080.2.1 SL3.0ch00     723860    A     C     Solyc00g005060.1     CDS     NONSYNONYMOUS     W/G     52    0    novel     DELETERIOUS (*WARNING! Low confidence)
Solyc00g005060.1.1 SL3.0ch00     723867    A     C     Solyc00g005060.1     CDS     SYNONYMOUS     G/G     49    1    novel     TOLERATED
Solyc00g005080.2.1 SL3.0ch00     723867    A     C     Solyc00g005060.1     CDS     SYNONYMOUS     G/G     49    1    novel     TOLERATED
Solyc00g005060.1.1 SL3.0ch00     723903    T     C     Solyc00g005060.1     CDS     SYNONYMOUS     G/G     37    1    novel     TOLERATED

Its results match the desired output except for the two mentioned lines plus, mayhap, the field separators (which weren't specified, btw).
 

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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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