MapRoutines.pm

        package MapRoutines;
        use strict;
        use warnings;
        use Bio::SeqIO;
        use IO::String;
        use File::Slurp;

        use Exporter;
        use base qw( Exporter );
        our @EXPORT_OK = qw( get_gene translateToProt );

        sub get_gene{
                my ($genomeHash,$gbkHash,$ID,$ext_start,$ext_stop) = @_; 
                #The soubroutine will retrieve a subseq (e.g. a gene) from a genome
                #Arguments: 1 = path to genome, 2 = %gbkhash, 3 = protein_id, 4 = extension of startposition backwards (optional), 5 = extension of stop position (optional)

                my $specieID = $gbkHash->{$ID}[5];
                if (not defined $specieID) {
                        die "Error: The protein id $ID was not found in any annotation file";
                }

                my $genomeHash_value = $genomeHash->{$specieID}; 
                if (not defined $genomeHash_value) {
                        die "Error: The species id $specieID was not found in any genome file";
                }
                my $genome_string = ">$specieID\n" . $genomeHash_value;
                my $io = IO::String->new($genome_string);
                my $genome = Bio::SeqIO->new(-fh => $io, -format => 'fasta');
                my $gene;

                while (my $seq = $genome->next_seq){
                        #Start and stop positions from %gbkhash
                        my ($start, $stop);

                        #If gene is on complementary strand, take the reverse complement of the seq
                        if($gbkHash->{$ID}[2] == 0){ 
                                $start = $gbkHash->{$ID}[0] - $ext_start;
                                $stop = $gbkHash->{$ID}[1] + $ext_stop;

                                $gene = $seq->subseq($start, $stop);
                        }   
                        else{
                                $start = $gbkHash->{$ID}[0] - $ext_stop;
                                $stop = $gbkHash->{$ID}[1] + $ext_start;

                                my $gene_obj = $seq->trunc($start, $stop);
                                my $reversed = $gene_obj->revcom;
                                $gene = $reversed->seq;
                        }   
                }   
                return $gene;
}

sub translateToProt {
	my $sequence = $_[0];
	my $DNA = Bio::PrimarySeq->new ( -seq => $sequence ,
					 #-id  => 'YP_989117.1',
					 #-accession_number => 'X78121',
					 -alphabet => 'dna',
					 -is_circular => 0 );
	my $protein = $DNA->translate;
  	#print substr $protein->seq,0,-1 . "\n";
	return substr $protein->seq,0,-1;
}
1;