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Created with Raphaël 2.2.029Oct28272522212019181513121187654130Sep2928272016151413109862131Aug2725242220191816151312111096543230Jul2928272623222120191615141312987652130Jun292825242322211816151411109872127May26252421201817151413121110864230Apr292827262322212019181614138765421removed print statementsdependent xref fixed (still need to sort out protein_id though)self before xrefs in delete_by_sourcenow saves results to databaseadded get valid_codes method to return a hash of accessions that are like the source name and of the right speciesuse the same goup name and not snp to get the snp adaptor in the Slice. This way you will get the ProxySnp adaptor and not a specific onefirst draft of GO parsingadded method get_species_id_for_filenameget and pass species to run methodAdded species specification and validation.GO removed. EMBl used to get protein_idsadded some basic sources for human and mouse. Will add rest as needs beordered added to source to order the processing. Also species_id added to source_url to allow processing by species onlyAdded dog & cow.Added aliases column to species tableAdded vaildation of source names.Added ability to specify database connection parameters on command line.Delete previous xrefs from this source when run directly.Fixed the seq_region_idx index in dna_align_feature/protein_align_feature to be compliant with table.sqlAdded a missing AffyRemoved deletion step before uploading new xrefs.Added hierarchical deletion of xrefs and associated objects. Currently only works for single-source use case. Need to think about how to handle when run from BaseParserVarious modifications for multi-source xrefs.Generalised SwissProtParser.pm to be able to generate SP and SPTR xrefs from the one fileUpdated to have separate sources for UniProtSwissProt and UniProtSPTrEMBL.Replaced by UniProtParser.pmCopied from http://www.ensembl.org/homepage_SSI/whatsnew/ens25/update_to_schema25.sqlAdded modification on external_db and density_feature tables25_26 patch sql*** empty log message ***Improved output formatting.Filter out non-SwissProt records (where ID line <> "STANDARD")Changes to RYO format output needed for calculating identities to go into identity_xref;Now properly calculates identities and filters on them.Changed method of identifying pseudogenes.doc changessub alias_exists added. returns 1 if it exists else 0Now compares by xref and my ensembl ID, and dumps those mapped by old/new method only to files.add sub to change the access fro a db connection*** empty log message ***