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Full Discussion: Matching two files with special field separator
Top Forums Shell Programming and Scripting Matching two files with special field separator Post 302878863 by Homa on Monday 9th of December 2013 09:38:43 AM
Old 12-09-2013
Oh, thanks, but now, there is another problem, in my actual file, the content of each of the headers is longer than one line, for example:

Code:
>ENSGALG00000014675|ENSGALT00000023647|1|1603|1605
cttttccactttgctctcatcCTGCTATTGGATTTgagatgcatgtcTGTTAATATTGTA
GCCTTTGGAAATGAAAGAGATGGATTTTCTGAAGACAATCAGCAGTCAAGTCTGATCTGG
AGCTATCTAGGGAGAAGTGCTCTCATTTCAGAGACTGAAAGTGGTCTGTTGCTGAATTCT
GCCAATCACATTAGAAATCCTGTTTTTACTGAATATCAAGCCTGCGTGTTTGGAAATGTC
AGATTGGTGGTACATGACTGTCCTCTTTGGGATATATTTGACAGTGACTGGTATACTTCT
CGCAGTCTCATTGGAGGAGCTGATATTATTGTGATTaaatactctgtcaatGACAAGACT
TCATTTCAAGAATTAAAGGACAGTTATGTCCCAATGATAAAAAAAGCGTTAAACCACTGT
TCAGTTCCAGTAATAATTTCTGCTATTGGTGCAAGAAAAAATGTGCCTTGTACCTGCCCA
CTGTGCACTTCAGACAGAAGGAGCTGTGTTACTTCTTCTGAAGGAGttcagcttgctaaa
gaactaggagctacgtatcttgaattgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnggaatattttatgatccaaagTTTGAATCGGAAGTCATCTGAAAAA
ATGAAGAAAAGAAGAAAGACCCAGAAGTACCATCGAGTTAAACCCCCTCAGCTTGAACAA
CCAGAAAAAATGCCAATCTTAAGAGGTGAAGCCTCACATTATGACTCTGATTTACACAAG
TTGCTGTCCTGCTGCCAGTGTGTGGATGTGATATTTTACTCAGAAGACTTAAAGAAAGTA
GTAGAAGCTCACAAGATCATTTTGTGCTCTGTAAGCCATGTCTTCATGTTACTTTTCAAA
GTGAAGAGTCCAGCTGATATTCATGATTCTGCTATCATACGGACTGCGCAAAGTCTCTTT
GCAGTGAACAGTGAAGCTGTGTTTCCGTTTCCTAGCAGTGGCTCATCATGCGACCCACCA
GTAAGAGTCATTGTTAAAGACTCCATCTTCTGTTCTTGTTTGTCAGACATTCTACACTTC
ATTTATTCAGGTGCTTTCCAGTGGGAACGGTTAGAAGAAGATATAAAGAAGAAGCTAA

Using this script:
Code:
awk -F"|" 'FNR==NR{A[">"$1];next}($1 in A){print;getline;print}'

prints only the first line of each content, is there a way to solve this? thanks!
 

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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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