Added support for the new 'gencode_primary' transcript attribute

[sgiorgetti]

Description

A new transcript attribute "gencode_primary" has being introduced (for human).
This attribute is meant to eventually - i.e. in the long run - replace GENCODE basic.

This change is necessary to support the displaying of the new attribute on the web site, as well as having it available in the published annotation files.

Use case

Check a transcript for the "gencode_primary" attribute.
This is entirely similar to the already available check for the GENCODE Basic attribute.

Benefits

It's a must have to properly handle the new attribute.

Possible Drawbacks

None

Testing

The test suite ran fine. Attribute testing is covered already by the existing suite.

[nwillhoft]

The example and subroutine names in the newly added code need updating from gencode_basic to gencode_primary

[nwillhoft]

Do we also need to remove this tag-based line (3145) as it's not used anymore?

$summary_ref->{'tag'} = 'basic' if $self->gencode_basic();

[nwillhoft]

@sgiorgetti Do we need to define type for this mane_transcript object? I can see in the REST server that type is available and printed out but I wasn't sure where it's being defined, and if it needs to be defined here?

[sgiorgetti]

@nwillhoft thanks for bringing this up. Reporting here the result of our discussion for the records.
The mane_transcript Transcript method returns a MANE object, which has the type method defined in it. This latter method returns the "type" of MANE - i.e. "MANE_Select" or "MANE_Plus_Clinical".

[nwillhoft]

Changes to modules/Bio/EnsEMBL/Transcript.pm look good. A gencode_primary subroutine has been added in to identify whether a transcript has a GENCODE Primary attribute. A typo in the gencode_basic subroutine has been fixed. Tags have also been added to summary_as_hash to provide transcript-related info for: MANE, canonical, GENCODE Basic and GENCODE Primary properties.