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Created with Raphaël 2.2.03Sep30Aug2924232221201716151413109876432131Jul3027262524232019181613119543229Jun282726252322212019181514131211876131May30292824232221171615141098632127Apr26252423201918171613121110543130Mar292827Adding patch from James Allen where a copy/paste bug has meant the incorrect setting of end_Exon to be on the $translation and not alternative $translationwrong database name usedmisc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pmAdded correct logic name. Production DB also updated.warn if you're working on the live db serverincrease width of param tableadded failsafe, do not get repeat features if slice is too bigsome disconnection for safetyUnfinished first effort at script.got the key and value invertedDelete uniparc xrefs and object_xrefs before uploading the mappingsAdded original stable ID for reference.missing run_all and max_run optionsadded a get_total method for snp densityadjust the total count summinginsert ignore so it does not complain if an alias already exists in the databaseadding the right values in the right orderUse correct coordinate system version.Removed caching for memory conservation.check length before coord_systema bit of text formattingadded trinomial database name supportOverride set_methods for WormBase species to allow non-exact matching to Uniprot recordsWhen creating the backup table, use CREATE TABLE LIKE and INSERT SELECTTidying up.typomessages a little bit more informativeif there is no previous database, no mapping neededNew eval mode. Seems to work for us.cvs/attic/Root_…cvs/attic/Root_branch-ensembl-xrefconfigWe MUST allow empty attributes to be storedStricter checking semantics.for method transcript_display_xref_sources, updated the ignore setup to be consistent with refactoring of DisplayXrefs.pmadded a new species, physcomitrella_patensAllowed for absence of Stable IDs in otherfeatures databases. Added dbID to debug prints.Removing warningsNow can search DBs more than just otherfeaturesAllow users to ignore seemingly wrong coordinatesget non reference slices when using split_chromosomes_by_size in the density scriptsget non reference slices when using split_chromosomes_by_size in the density scriptsstore only if value if positive