#!/usr/bin/perl -w

use strict;

# create_gff.pl, last update:  8/5/03
# creates a gff file from other files
# by Chet Langin, clangin@siu.edu
# SIU Plant Biotechnology and Genome Core-facility

# set the timer
use Time::HiRes;
my $start_time = Time::HiRes::time;

# all of the filenames are preset
# the output file will remain open throughout the script
# the input files will be opened and processed one at a time

open OUTPUT_FILE, ">soybean.gff"
  or die "Cannot open output file:  $!\n";

print "Current file being processed:  MLG\n";
open MLG_INPUT, "<../gff/mlg.gff"
  or die "Cannot open MLG file:  $!\n";
# copy each line as is to the output file
while(<MLG_INPUT>) {
  print OUTPUT_FILE;
} # while
close MLG_INPUT;

my @file_list = qw/ sorted_locus_placements.txt sorted_clone_placements.txt sorted_contig_placements.txt/;
my $track = "";

foreach my $current_file(@file_list) {
  if($current_file =~ /locus/) {
    $track = "Loci";
  } # if
  elsif($current_file =~ /clone/) {
    $track = "Clone";
  } # elsif
  else {
    $track = "Ctg";
  } # else
  print "Current file being processed:  $track\n";
  open(CURRENT_INPUT, "<", $current_file)
    or die "Cannot open $current_file:  $!\n";
  while(<CURRENT_INPUT>) {
    chomp;
    my @fields = split /\t/;
    my $mlg = $fields[0];
    my $start = $fields[1];
    my $end = $fields[2];
    my $name = $fields[3];
    print OUTPUT_FILE "$mlg\tvarious\t$track\t$start\t$end\t.\t+\t.\tSequence \"$name\" ; Note\n";
  }
  close CURRENT_INPUT;
} # foreach

close OUTPUT_FILE;

# show the run time
print "Run time:  ${\(Time::HiRes::time - $start_time)} seconds\n";