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Full Discussion: Match substring from a column of the second file
Top Forums Shell Programming and Scripting Match substring from a column of the second file Post 303003171 by yifangt on Friday 8th of September 2017 01:01:27 PM
Old 09-08-2017
Match substring from a column of the second file
I want to merge the lines by matching substring of the first file with first column of the second file.
Code:
file1:

S00739A_ACAGTG_L001_R1.fq.gz
S00739A_ACAGTG_L001_R2.fq.gz
S00739B_GCCAAT_L001_R1.fq.gz
S00739B_GCCAAT_L001_R2.fq.gz
S00739D_GTGAAA_L001_R1.fq.gz
S00739D_GTGAAA_L001_R2.fq.gz
S00739E_ATCACG_L001_R1.fq.gz
S00739E_ATCACG_L001_R2.fq.gz

Code:
file2:

S00739A WT-1
S00739B WT-2
S00739D mt-1
S00739E mt-2

output:
Code:
S00739A_ACAGTG_L001_R1.fq.gz WT-1
S00739A_ACAGTG_L001_R2.fq.gz WT-1
S00739B_GCCAAT_L001_R1.fq.gz WT-2
S00739B_GCCAAT_L001_R2.fq.gz WT-2
S00739D_GTGAAA_L001_R1.fq.gz mt-1
S00739D_GTGAAA_L001_R2.fq.gz mt-1
S00739E_ATCACG_L001_R1.fq.gz mt-2
S00739E_ATCACG_L001_R2.fq.gz mt-2

This is my try, but this part has problem A[1]=$0 that makes the script invalid:
Code:
awk 'FNR==NR {split($1, A, "_"); A[1]=$0; next} {print A[$1], $2}' file1 file2

Thanks for any help!
Last edited by yifangt; 09-08-2017 at 02:10 PM.. Reason: explanation
 

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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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