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Code updated to implement review comments. There is a new package to handle stop codon readthrough in a sequence. Test case has been updated with new regex

The previous test-database update missed some patches for the core and
variation schemas, which is why Travis jobs keep failing these days.

ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X

Code updated to implement review comments. There is a new package to handle stop codon readthrough in a sequence. Test case has been updated with new regex

The previous test-database update missed some patches for the core and
variation schemas, which is why Travis jobs keep failing these days.

ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X

See ENSCORESW-3054. Only really affects the test suite at this point,
in the code proper the prefix only appears in docstrings.

Apply patch_96_97_{c,d,e}, insert the necessary data into
homo_sapiens/core.

Quote noisy strings properly + avoid double-sigil dereferences.

Properties of specific types of mature RNA products such as microRNAs
are stored in the database as attributes (so that we needn't add
type-specific columns to the rnaproduct table) but have shorthand
accessors such as MicroRNA::arm() backed by cache member variables
in the API (for convenience and speed). In order for this to work
properly we have to push possible changes to the cache variables back
to attributes before they are stored in the database - which is what
this method does.

The synchronisation code itself is generic and has been implemented
in the superclass. Specialisation is handled by class-specific mappings
between member names and respective Attribute codes, provided
by RNAProductTypeMapper.

Limitations:
 - at present there can only be either zero or one target attribute;
   having many attributes with the same code results in an exception
   because we do not know which one(s) to update. In the future we might
   have to extend the mapping syntax to support multiple attributes, for
   now however (i.e. for microRNA arms) we do not need it;
 - chances are things will break badly if we fetch a MicroRNA object
   from the database, change the arm and push it back. Right now this is
   not a problem because RNAProducts do not support database updates at
   all, then again should we want to support them we will have to check
   how AttributeAdaptor handles updates of existing objects (as well as
   the same for DBEntryAdaptor, as a matter of fact).

On the one hand there seems to be no good reason for a MicroRNA object
having multiple arm attributes, on the other hand simply taking the
first one in the event of it happening may not even return the same
value every time (it depends on a lot of factors, from the
implementation details of AttributeAdaptor up to and including the
underlying database system). There was a warning but who reads those
anyway. Just throw an exception instead, if someone decides to allow
such a case they can always catch it.

Doesn't really matter since this xref was processed entirely offline -
but just in case.

Previously, get_all_Attributes() would throw an exception in the event
of absence of both the local attribute cache and the adaptor link. That
was not entirely correct because a locally created RNAProduct object
which has not been assigned any attributes would look exactly like that.
get_all_DBEntries() got that right so let's follow its example.

Having carefully analysed miRBase data for mature microRNA products
corresponding to stem-loop sequences already present in Ensembl, I
confirm that the calculation of their start and end in genomic
coordinates is indeed correct for when the stem loop originates from
both forward and reverse strand.