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Created with Raphaël 2.2.023Apr22212015149872131Mar262524191817161312119654326Feb25191817161110985432130Jan292726222120191615147618Dec171311109865432126Nov252421201817141312111087654331Oct3029272421201716151310976229Sep23221812109852127Aug26212019181513121198765432131Jul2928262524232221181716151412111097432127Jun26252416131110965432130May292322212019161512987529Apr28add marmoset analysesnew set of sql statements to remove tmp and bak tables used during mapping processupdated documentation with cleanup scriptadded option -pattern to allow running the script in a group of databasesscript that will calculate if the assembly table has overlapping regions in same coord_systemmerge from vega-49-devmerge from 49-devRemaining part of db_display_name added for Tgut_symbol.Entry added for Tgut_symbols. These are the gene symbols assigned to Taeniopygia guttata (zebra finch) genes by Dave Burt.added FOS ends for zebrafishDocumentation edited for get_original_seq_region_positionminor tweaksDescription file and script to load the misc set descriptions to a databasewhitespace*** empty log message ***cvs/release/ens…cvs/release/ensembl/53 release/53 upstream/release/53Document that the definition for a term is optional.moved analysis_id key from id_xref to oxref*** empty log message ***method to cleanup blast databaseuse ncRNA database now instead of the species files, which had to be manually copied overnew parser to get ncRNA xrefs from the newly created xref ncRNA databaseFinish implementation of fetch_ancestor_chart():change of ccds and vega databasesignore MGI starting with OTTMUSG as these should not be in the xrefswhole new rewritepretty much a rewrite.$ missing before xref_countnew test code to calculate display xrefs using the xref database and SQL only. So much, much faster as just simple sql instead of gettin gall genes, then all transcripts then all dbentries. Caveat though is that all the xrefs have to be in the xref database and cannot be used to an update mode. i.e. just adding one particular source. Can only be used whan adding ALL sources possible.use object_xref_id to join dependent xref to object_xref and not xref_id as this is more unique. Interpro GOs do not have dependent_xrefs so GOs need to be processed slightly differently by doing a left join insteadrececlaration message removalset dumped to be 100 and not 0 just to be sure.move all MGI to genes to start with and make sure transcript names are unique.remove entries from analysis_description using logic name instead of display labelSimplify much of the SQL.Throw exceptions where appropriate.Tiny POD fix.removing indels until they get fixedDon't go through dbc() to get prepare().Make children() and parents() take a list of strings representing theFixed spelling.