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Created with Raphaël 2.2.02Sep127Aug26212019181513121198765432131Jul2928262524232221181716151412111097432127Jun26252416131110965432130May292322212019161512987529Apr2825242322211817161514111084326Mar25232019181714131211629Feb282722212019141211765131Jan29282524232221181715141110987321Dec201918171413121130Nov292827232221201716151413129876verbose addedscript: now added to replace LOCAL: or file: to generate the files and not use the local files-verbose option added which also need to change run subroutine to get the file/s via a ref to and array then an arrayrun changed to run_script to get the information via a series of mysql and perl instead of from a local filenew moduleadded new tests to check attributes db_name and db_display_name work properly to retrieve the database_name and the displayable_name from the external databaseadded 2 new attributes in protein and dna alignFeatures to get the name of the external database and the displayable nameremoved helpdesk_draft.txt, analysis_descriptions_draft.txt to avoid confusion. The file to use with load_analysis_descriptions.pl is analysis.descriptions.Giulietta's changes to the make the analysis descriptions more informative.reset wording of links to Havana transcriptsupdated analysis description from helpdeskupdate analysis descriptionFix typo.add primary ids for HGNC and not the display names twice.Read new format file: tab separated, and with display_label as 3rd column.Changed format to be tab-separated and added display_label as third column (default is logic name with _ removed).added option to pass a reference to an array as argument in fetch_all_by_biotypeadded 2 new tests for the fetch_all_by_biotype methodAdded slothChanged GeneNo_IgSeg code to GeneNo_Ig, due to a biotype change in human and mouse where all IGChanged creation of compara adaptor in get_all_compara_Syntenies and get_all_compara_DnaAlignFeatures to use registry directly.small fix to 2 typosSet gene description to NULL and status back to KNOWN_BY_PROJECTION when deleting previously-projected xrefs.added new column external_data for user upload databaseadded functionality to allow turning off caching of most recent features*** empty log message ***Added two new types used during the Havana-Ensembl gene mergeMore informative output.Refactored - do names and GO terms in one job for those species where both were done separately before. Should reduce the number of jobs.bind_columns() misspellt as well.... urghMisspellt variable name, fixed.New method on the DBAdaptor, mostly useful for multi-species databases:Mainly small bug fixes and removal of commented out codename change 'Clone_based_ensembl_transcri' now 'Clone_based_ensembl_transcript'check for refSeq_dna being predicted before saving and save as predicted if soadded ensembl_mapped from hgnc filesub add_to_direct_xrefs addedprint out options so to make it easier to keep track of what has been ran. And run the cleanup script after running coordinate mapping so that xrefs only on one coordinate system