With some pattern matching perhaps

#!perl
use strict;

# replace with Getopt::Long code as before
my $vars = {
  seq1 =>'USER_INPUT.txt',
  seq2 => 'USER_INPT2.txt',
  ref => 'USER_INPUT_REF.txt',
  chr_list => 'USER_INPUT_CHR.txt',
};
 
my $input = 'template.config';
open IN,'<',$input or die "Could not open $input : $!";
my $output = 'new_'.$input;
open OUT,'>',$output or die "Could not open $output : $!";

while (<IN>){
  chomp;
  # match selected lines
  # and append "value"
  if (/^ *\$;(Seq\d|Ref|Chromo).*\$; =/){
    my $key = ($1 eq 'Chromo') ? 'chr_list' : lc $1;
    $_ .= '"'.$vars->{$key}.'"';
  }
  print OUT $_."\n";  
}
close IN;
close OUT;

[download]
poj

In reply to Re^5: Read in a template file, populate using user input and and generate a new file by poj
in thread Read in a template file, populate using user input and and generate a new file by Bioinfocoder

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