#!/usr/bin/perl -w

use strict;

# adjust_loci_file.pl, last update:  7/23/03
# Adjusts the previously made loci.gff file to a more usable format
# By Chet Langin, clangin@siu.edu
# SIU Plant Biotechnology and Genome Core-facility

# start timer
use Time::HiRes;
my $start_time = Time::HiRes::time();

# check arguments
if(scalar(@ARGV) != 2) {
  print "Usage:  ./adjust_Loci_file.pl input_file output_file\n";
  exit;
} # if
my $input_file_name = $ARGV[0];
my $output_file_name = $ARGV[1];

open(INPUT_FILE, "<", $input_file_name)
  or die "Cannot open input file:  $!\n";
open(OUTPUT_FILE, ">", $output_file_name)
  or die "Cannot open output file:  $!\n";

while(<INPUT_FILE>) {
  chomp;
  s/^\s+//;
  s/\s+$//;
  my @old_fields = split /\t/;
  my @new_fields = ();
  $new_fields[0] = $old_fields[0];  # MLG
  $new_fields[1] = sprintf("%08d", $old_fields[3]);  # start
  $new_fields[2] = sprintf("%08d", $old_fields[4]);  # end
  my $midpoint_float = $old_fields[3] + (($old_fields[4] - $old_fields[3]) / 2);
  my $midpoint_int = sprintf("%08.0f", $midpoint_float);
  $new_fields[3] = $midpoint_int;
  my $name_field = $old_fields[8];
  $_ = $name_field;
  my @name_array = split /"/;
  my $name = $name_array[1];
  $new_fields[4] = $name;
  my $output_line = join "\t", @new_fields;
  print OUTPUT_FILE "$output_line\n";
} # while

close INPUT_FILE;
close OUTPUT_FILE;

my $run_time = Time::HiRes::time() - $start_time;
print "Run time:  $run_time\n";