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Created with Raphaël 2.2.013Nov129876532131Oct3029262524232218171615121098543128Sep2725242118171413121110654330Aug2924232221201716151413109876432131Jul3027262524232019181613119543229Jun282726252322212019181514131211876131May302928242322correct rat aliasmissing end of line for piggy sourceupdate ensembl_ontology to schema 70UniGene source for microbat does not exist any morenot using ensembl clone name if official name is not HGNC, MGI or ZFIN_IDPOD cleanupBugfix? Previous revision of this script assumed that we could have only one ensembl_id (gene) associated with an OTTG. This is not true as projected genes have the same OTTG attached to them as theier parent gene on the primary assembly.Attempt to speed up. Previous use of Algorithm::Diff was prohibitively slow, so attempting to use bitmasking on simple cases to go 10x faster on the easy cases.Might as well log the numbers of "new" canonicals along with the old ones that were updated.Missed out adding orphan canonical IDs to the change_list.Missing _ in cache key.Added in taxon id cache value updating to prevent it resetting itself in subsequent calls.Fix for production team, for whom changing taxonomy ids (Gorilla) caused it to leave old metadata behind. Failure triggers an attempt to guess taxon id by regexing the end of the dbname off and searching by that instead of taxon id.added methods to get count on alternate sequencesadded methods to get gene counts on alternate sequencesreplaced gene count with generic countAdding processed_pseudogene to our groupsHave changed the link for the SO.obo file from http://downloads.sourceforge.net/project/song/Sequence%20Ontology/so_2_5/so.obo2.5 to http://www.sequenceontology.org/resources/obo_files/current_release.obo. This will allow us to get the most up to date version.Have updated the link to get the EFO.obo file from http://www.ebi.ac.uk/efo/efo.oboSHIP IT! EFO now loads in without complaints from OBOParser. Also now handles duplication relations being inserted.Warnings made to go away... one hack to complement another.Added missing record terminator in diagnostic log.Using undef instead of '', because '' gets flattened in eval.Added support for situations where original canonical transcripts have disappeared from the data.Added a truth test to see if the $term->{synonyms} reference was there. I'm assuming if it's there then it'll be an arraySwitched to Test::More and done_testing(). This should stop tests from failing due to poor test count specification.Switched to Test::More and done_testing();Make the verbose doc a bit more verbose. People in workshops could not find this method which points to poor documentationrevert back to version 1.13updated regular expression as was not matching lrg url any moreAdded meta insert as otherwise any schema generated from this file would break when being patched. Also changed the ordering of the fields in protein_feature to avoid poor patch performanceTest schema now matches live. Any future patching should be done using the ensembl-test/scripts/patch_test_databases.pl script.First pass at summary stats.use Test::More rather than old Test library. Avoids breaking tests when we change the numbers of tests runstarted release 70added hdescription to protein_featurepatched to v70reformatted to use new perltidy optionsImproved speed of DensityGenerator by using new count methodsreformatted to use new perltidy options