my %inputfiles = (
    gene2accession => join( "\t",
        qw( Taxon
            GeneID
            Status
            RNA_Nucleotide_Accession
            RNA_Nucleotide_gi
            Protein_Accession
            Protein_gi
            Genomic_Nucleotide_Accession
            Genomic_Nucleotide_gi
            Genomic_Accession_Start_Pos
            Genomic_Accession_End_Pos
            Orientation
            Assembly
        )
    ),
    gene2go => join( "\t",
        qw(
            Taxon
            GeneID
            GO_ID
            Evidence
            Qualifier
            GO_term
            PubMedID
            Category
        )
    ),
    ...
);

foreach my $file ( keys %inputfiles ) {
    ...
    while ( my $line = <INPUT> ) {
        if ( $linecount == 0 ) {
            print OUTFILE "$file\n";
            print SUMMARY "Field lengths for file $file\n";
            print SUMMARY "$inputfiles{$file}\n";
            if ( $file eq 'hiv_interactions' ) {
                # do special processing
            }
        }
    }
    ...
}