GitLab

is_canonical() can lazy-load the value from the database when it is unset & a dbID and an adaptor is available.

has unrelated remark beginning with string "selenocysteine ". Found to be the
case in OTTDART00000030742 for Dec 19th 2011 Havana data-freeze of Zebra fish.

First stage commit only. Partial functionality (detailed below), but works and reduces
chance of missing problems.

1. Made exception data structure richer for check_for_stops to allow a number of different
types of exception to to be expressed.

2. Added a new exception type, that of known TGA-stopping Sec-coding transcript.

3. Added data-structure to add_selcys stop checking to allow specification of known
TGA-stopping Sec-coding transcripts.

1. Fix check_for_stops to cope with multiple adjacent internal stops without a loss of codon to AA sync.
Found when running add_selcys.pl on zebrafish for Vega 47.

2. Fix to existing conditional in vega Sec QC script which tests for an anacode bug before deciding to complain
about missing Sec markup for selenoproteins that also stop with TGA, so that this conditional actually spots
this case in more proteins and so cries wolf less often.

unique genes method (for assembly patches), interactive does have an argument, other binaries default to 1 if nothing specified

toplevel location code can now deal with excessively large regions and shrinks them down to size if possible or rejects them.

load_XXXX() methods now return the number of adaptors which have appeared in the registry due to that method's invocation. This can be used to report success or failure to load databases.

Improving the error handling of the DBI connection in load_registry_from_db(). We now report an error if it cannot connect to the MySQL DB and if it was not pingable. Hopefully this catches both erronious scenarios.

similarity events.  Require similarity events to be within 1.5% (not 2%)
of top score.

Reformat routine while here.

Bigger penalty for exonerate matches on other seq_regions.

Rescore penalty altered to 0.9.

gene rescore penalty from 0.8 to 0.9.

in the ananlysis table, return a reference to an empty list.  Without
this change, all features would have been returned which would quickly
make the client run out of memory.

added fetch_all_by_name which gets all the xrefs that have the accession, display_label or synonym that is passed to it. external database source is optional

warning if species alias is not found.

In get_DBAdaptor(): Thow exception if species alias not found (excactly
as in get_adaptor()).