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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 302978378 by cpp_beginner on Friday 29th of July 2016 12:38:12 PM
Old 07-29-2016
Help with merge data with a reference sequence
I have two input file.:

File 1 is a large reference sequence (A large Fasta sequence);

File 1 (is a file which first line is the header description and line other ">" is its corresponding word and counting from 1 till end of file);
Code:
>Data_1
ASWDADAQTWQQGSAAAAASDAFAFA
.
.

File 2 is list of data that I interested to replace specific word at specific location in File 1;
File 2 (3 column in File 2 and is tab-delimited format);
Code:
Data_1 2 Z
Data_1 3 T
Data_1 10 A
Data_1 11 T
.
.

Desired Output File
Code:
>Data_1
AZTDADAQTATQGSAAAAASDAFAFA
.
.

File 1 is a long record Fasta file (Include a first line of header description and line after ">" is its corresponding word).
File 2 is a file got 3 column (Tab-delimited).
First column is the header description (without ">") of File 1;
Second column is the position of word that I wanna to replace in File 1 based on Third column data;
Third column is the word that I wanna to replace it which specific word/specific position of File 1;

Awk code try
Code:
awk -F "\t" '(FNR==1){x++} (x==1){a[$1][$2]=$3;next} (x==2){if($0~/>/){h=$0;sub(/^.*Data/,"",h);sub(/ .*/,"",h)} else{seq[h]=seq[h]$0}} END{for(i in a){s=0; for(j in a[i]){m=m substr(seq[i],s,j-1) a[i][j];s=j+1} m=m substr(seq[i],s); print ">Data"i"\n"m}}' File 2 File 1

I would like to replace specific word (exclude header >Data_1) at specific location in File 1 if it is list on File 2 data.
My main objective is hope to replace specific word at specific location in File 1 based on the record provided in File 2 (specific position and replace with new word based on File 2).

Thanks for any advice.
Last edited by cpp_beginner; 07-31-2016 at 12:04 PM.. Reason: Corrected code tags.
 

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LEARN ABOUT MOJAVE

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 v5.18.2							    2014-01-06						File::Spec::Functions(3pm)
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