#!/usr/bin/perl -w
# Open Tab-delimited file, extract and display HOX gene info
#FILE HANDLING
open INPUT,"<MOUSE_TF1.txt";    
open OUTPUT,">HOX_GENE_TF.txt";   
#
# MAIN
print OUTPUT "MOUSE TRANSCRIPTION FACTORS IN THE HOX GENE FAMILY\n\n\n";
print OUTPUT "ENSEMBL GENE ID \tSYMBOL \tCHR\tSTART\t\tEND\t\tSTRAND\n";
while (<INPUT>){
  $line = $_;
  chop($line);
# split line by tab character
  @Gene_Info = split("\t",$line);            
# Defines fields as scalars
  $Ensembl_Gene_ID = $Gene_Info[0];          
  $Chromosome_Name = $Gene_Info[1];
  $Gene_Start = $Gene_Info[2];
  $Gene_End = $Gene_Info[3];
  $Chr_Strand = $Gene_Info[4];
  $Gene_Symbol = $Gene_Info[5];
# Create hashes to store table values and associate with key
  $chrs{$Ensembl_Gene_ID} = $Chromosome_Name;
  $starts{$Ensembl_Gene_ID} = $Gene_Start;
  $ends{$Ensembl_Gene_ID} = $Gene_End;
  $symbols{$Ensembl_Gene_ID} = $Gene_Symbol;
  $strands{$Ensembl_Gene_ID} = $Chr_Strand;
  }
close INPUT;
# select Gene Symbols belonging to "Hox" family and print
foreach $key (keys %symbols) {
  if ($Gene_Symbol =~ /Hox/) {
 	print OUTPUT $key,"\t";
        print OUTPUT $symbols{$key},"\t";
        print OUTPUT $chrs{$key},"\t";
        print OUTPUT $starts{$key},"\t";
        print OUTPUT $ends{$key},"\t";
        print OUTPUT $strands{$key},"\n";
   }
}
close INPUT;
close OUTPUT;
#end