re implemented convert_peptide_coordinate_to_contig. Will be renamed to pep2genomic soon. Should work similarily to cdna2genomic

Can now retrieve genes in chromosomal or RawContig coords from core GeneAdaptor::fetch_by_stable_id

prediction_transcript->translate now returns a Bio::Seq like in transcript, instead of the actual peptide sequence

made sure exons get analysis objects before being added to gene

in translate now strip terminal stop codons from mrna before making Bio::Seq out of it

translateable_seq does still return sequence  with stop codon on the end

script.

genes in chromosomal coords from fetch_by_stable_id

database used for transform is _always_ taken from slice/contig (i.e. not feature or exon)
tidied up a bit in SeqFeature and BaseAlignFeature

Gene start/end/strand/chr_name convenience accessors improved a bit (warning only if gene spans contigs)