Updated fetch_all_by_Transcript method to optionally filter by featur…

Check that translations exist before comparing the sequences

If a translation object does not exist, we do not try to access its sequence

Check that an analysis exists before calling logic_name on it, needed for testing where a full object might not exist. And just good sanity.

New Transcript added to the test file transcript.txt. So updated the tests that checks for the transcript count.

Updated fetch_all_by_Transcript method to optionally filter by feature_type (dna_align or protein_align features)

Add seq_region_start and seq_region_end to Slice, as a Slice is always relative (or is) a toplevel coordinate system, a simple alias to start/end() are possible.

New attrib table for dna_align_features

Add get_Gene() method to CDS, ExtonTranscript and UTR objects to match Transcript method, for consistency in accessing.

Added source_dir and target_dir parameters allowing copy of databases outside the MySQL default internal directory on Sanger machines /mysql/data_3306/databases/. When target_dir is specified, the script will automatically create a symlink from target_dir to /mysql/data_3306/databases/. This change will allow us to copy databases from and to the new ens-staging3 MySQL server

This reverts commit cbd14e9f.

Compara test db for Slice methods

Changing all ens-staging1/2 to ens-staging3, as we'll be using this new host for pipelines until the EBI shift over