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Created with Raphaël 2.2.010Jan9654323Dec22212019141312987652130Nov292524232221181715121110987432131Oct28272625242120191817141312111076543230Sep29282726232221201615141312987652131Aug302625242322191817161512111098542129Jul2827262522212014produce stats on the quality of feature mapping between two assembliesload feature location in old db, new db and feature mapping between two assembliesUpdate year to 2012Adding in a script to make the yearly copyright notification update a bit easiernow catches schema versions as empty stringsAdded specific code for Scer for parsing the EC number from the description lineAttach SGD GO mapping to translation objectsAttach SGD mapping to translation object rather than transcript objects, so GO mapping get also attach to translations. Commented STDERR statements;deleted misplaced croak statementBug found meaning the specified target location was never used & the script would have brokenProxy for DBConnections. In to make sure code is not lost for the futureDeprecating get_Species() so tests need to be updatedDeprecating get_Species()Removing the use of get_Species()Code used to create dynamic proxiesadded species cavia_porcellusMore docsAdding a check to prevent unintentional dropping of mart tablesRemoved usage of get_Species()Removed as specified in release declarationsupdated readmeAvoid the lines starting by a comment character (# or --)Adding support for mart temporary tables and making the documentation clearerGiving this the option to specify the default location which should help when using these. Also switch to env perl and used warnings explicitly rather than rely on #! linesAdding an option to copy to a non standard location for use by teams who do not store their MySQL data in its data directorymissed out a patch identifierImproving documentationCleanup of code with brackets due to 5.14 issuesis_canonical() can lazy-load the value from the database when it is unset & a dbID and an adaptor is available.added biotype column to transcript_stable_idadded cshell script to generate commands for running LRGsupdate get_set_list to use ExonerateGappedBest5 method for RefSeq_mRNA and ncRNA (predicted) xrefsupdate get_set_list to use ExonerateGappedBest5_agam for RefSeq_mRNA and ncRNA (predicted) xrefscheck biotype before linking transcript to RefSeq_mRNA, RefSeq_ncRNA xrefsStore Clone_based_ensembl_gene descriptions last, to avoid an accession name conflict with Clone_based_vega_gene descriptions. Assign an HGNC name which hasn't been used if possible.populate biotype column in transcript_stable_id tableDon't remove core data if status is moved back to mapping_finished. Changes to alt_alleles: use the first non-reference gene if there is no reference gene in an alt_allele.load core data before mapping stageparse dependent infolink RefSeq_dna to mRNA and nc_RNA using dependent option