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Full Discussion: Help with merge data with a reference sequence
Top Forums Shell Programming and Scripting Help with merge data with a reference sequence Post 302978400 by Scrutinizer on Friday 29th of July 2016 04:51:25 PM
Old 07-29-2016
If fasta sequences are always only a single line:
Code:
awk '
  NR==FNR { 
    R[$1,$2]=$3
    next
  }
  FNR>1 {
    s=x
    for(i=1; i<=length($2); i++) s=s (($1,i) in R ? R[$1,i] : substr($2,i,1))
    print RS $1 FS s
  }
' file2 RS=\> FS='\n' file1



----
Note: FS= (the extension that if FS is equal to the empty string, each character becomes a separate field) is not part of POSIX and may or may not work with your version of awk.
 

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LEARN ABOUT SUSE

file::spec::functions

File::Spec::Functions(3pm)				 Perl Programmers Reference Guide				File::Spec::Functions(3pm)

NAME

       File::Spec::Functions - portably perform operations on file names

SYNOPSIS

	       use File::Spec::Functions;
	       $x = catfile('a','b');

DESCRIPTION

       This module exports convenience functions for all of the class methods provided by File::Spec.

       For a reference of available functions, please consult File::Spec::Unix, which contains the entire set, and which is inherited by the
       modules for other platforms. For further information, please see File::Spec::Mac, File::Spec::OS2, File::Spec::Win32, or File::Spec::VMS.

   Exports
       The following functions are exported by default.

	       canonpath
	       catdir
	       catfile
	       curdir
	       rootdir
	       updir
	       no_upwards
	       file_name_is_absolute
	       path

       The following functions are exported only by request.

	       devnull
	       tmpdir
	       splitpath
	       splitdir
	       catpath
	       abs2rel
	       rel2abs
	       case_tolerant

       All the functions may be imported using the ":ALL" tag.

COPYRIGHT

       Copyright (c) 2004 by the Perl 5 Porters.  All rights reserved.

       This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

SEE ALSO

       File::Spec, File::Spec::Unix, File::Spec::Mac, File::Spec::OS2, File::Spec::Win32, File::Spec::VMS, ExtUtils::MakeMaker

perl v5.12.1							    2010-04-26						File::Spec::Functions(3pm)
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