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Full Discussion: Help with replace character based on specific location
Top Forums Shell Programming and Scripting Help with replace character based on specific location Post 302505948 by pravin27 on Friday 18th of March 2011 04:57:11 AM
Old 03-18-2011
Try this,
Your reffile column should match with input_file.txt. I have added lowercase(lc). Hope this will resolved your problem.

Code:
#!/usr/bin/perl

my %ref_h;
my (@refdata,@ar);
my ($start,$end,$format,$col);

open(RF,"<","reffile") or  die "Fail-$!\n";
while (<RF>) {
chomp;
@refdata=split;
push (@{$refdata[0]},$refdata[1],$refdata[2]);
$ref_h{lc $refdata[0]}=\@{$refdata[0]}
}
close(RF);

open(DF,"<","/tmp/input_file.txt") or die "Fail-$!\n";
while (<DF>){
        chomp;
        if (/^\>/) {
        ($col=$_)=~s/\>//g;
        next unless exists $ref_h{lc $col} ;
        print "$_\n";
        next;
        }
        $index=$#{$col};
        for ($k=0;$k<=$index;$k++) {
        $start=$ref_h{lc $col}[$k];
        $end=$ref_h{lc $col}[++$k];
        substr($_,($start-1),($end-$start+1))="X" x ($end-$start);
        }
        print $_,"\n";
        $start=0;$end=0;$index=0;
}
close(DF);

 

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LEARN ABOUT OSX

findbin

FindBin(3pm)						 Perl Programmers Reference Guide					      FindBin(3pm)

NAME

       FindBin - Locate directory of original perl script

SYNOPSIS

	use FindBin;
	use lib "$FindBin::Bin/../lib";

	or

	use FindBin qw($Bin);
	use lib "$Bin/../lib";

DESCRIPTION

       Locates the full path to the script bin directory to allow the use of paths relative to the bin directory.

       This allows a user to setup a directory tree for some software with directories "<root>/bin" and "<root>/lib", and then the above example
       will allow the use of modules in the lib directory without knowing where the software tree is installed.

       If perl is invoked using the -e option or the perl script is read from "STDIN" then FindBin sets both $Bin and $RealBin to the current
       directory.

EXPORTABLE VARIABLES

	$Bin	     - path to bin directory from where script was invoked
	$Script      - basename of script from which perl was invoked
	$RealBin     - $Bin with all links resolved
	$RealScript  - $Script with all links resolved

KNOWN ISSUES

       If there are two modules using "FindBin" from different directories under the same interpreter, this won't work. Since "FindBin" uses a
       "BEGIN" block, it'll be executed only once, and only the first caller will get it right. This is a problem under mod_perl and other
       persistent Perl environments, where you shouldn't use this module. Which also means that you should avoid using "FindBin" in modules that
       you plan to put on CPAN. To make sure that "FindBin" will work is to call the "again" function:

	 use FindBin;
	 FindBin::again(); # or FindBin->again;

       In former versions of FindBin there was no "again" function. The workaround was to force the "BEGIN" block to be executed again:

	 delete $INC{'FindBin.pm'};
	 require FindBin;

AUTHORS

       FindBin is supported as part of the core perl distribution. Please send bug reports to <perlbug@perl.org> using the perlbug program
       included with perl.

       Graham Barr <gbarr@pobox.com> Nick Ing-Simmons <nik@tiuk.ti.com>

COPYRIGHT

       Copyright (c) 1995 Graham Barr & Nick Ing-Simmons. All rights reserved.	This program is free software; you can redistribute it and/or
       modify it under the same terms as Perl itself.

perl v5.16.2							    2012-10-11							      FindBin(3pm)
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