#!/usr/bin/perl
    use warnings;
    use diagnostics;
    
    # Title: convertDataToGeneSymbol.pl
    # Author: Nicholas Bense
    # Date: 11/4/15
    
    # Open a filehandle to read file #1
    open(INF1,"<",'/scratch/Drosophila/fb_synonym_fb_2014_05.tsv' ) or die $!;
    
    # Open a filehandle to read file #2
    open(INF2,"<",'/scratch/Drosophila/FlyRNAi_data_baseline_vs_EGF.txt') or die $!;
    
    # Open a filehandle to read file #3
    open(INF3,"<",'/scratch/Drosophila/gene_association.goa_fly') or die $!;
    
    # Open a filehandle to write new file
    open(OUTF1,">",'FLYRNAi_data_baseline_vs_EGFSymbol.txt') or die $!;
    
    # Initialize a hash for the gene symbol conversion
    my %geneSymbolConversion;
    
    # Read Input File 1 line by line
    while (<INF1>){
    
    # Get rid of whitespace
            chomp;
    
    # Split the line
            my @INF1Array = split("\t", $_);
    
    # Filter entries starting with FBgn
            while ($INF1Array[0] =~ /(^FBgn\d+)/){
    
    # Assign column 1 to hash key scalar
            my $geneID = $INF1Array[0];
    
    # Assign column 2 to hash value scalar
            my $geneSymbol = $INF1Array[1];
    
    # Assign key and value to hash
            $geneSymbolConversion{$geneID} = $geneSymbol;
    
    }
    
    }
    
    # Read Input File 2 line by line
    while (<INF2>){
    
            # Get rid of whitespace
            chomp;
    
            # Initialize key value in case it is not found
            my $geneSymbol = "NA";
    
            # Split the line on tabs
            my ($geneID, $EGF_Baseline, $EGF_Stimulus) = split("\t", $_);
    
            # Check if the codon is present in the hash
            if (defined $geneSymbolConversion{$geneID}){
    
                    # Get the value associated with the codon from the hash
                    $geneSymbol = $geneSymbolConversion{$geneID};
            }
    
            # Join data and print to output file
            print OUTF1 join( "\t", $geneID, $geneSymbol, $EGF_Baseline, $EGF_Stimulus), "\n";
    }