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Created with Raphaël 2.2.015Mar14131098763127Feb242322212017161514131098762131Jan302625242320191817161312119654323Dec2221201917161514131298652130Nov2928242322211817161514111098743131Oct282726252421201918171514131210765430Sep292827262322212019161513987231Aug262322191716151211985432129Jul282725222018141387654130Jun29272422212017161514131098732131May27262524201918Now throws if a dependent_xref is found, but the source (EntrezGene|MIM) are not in the xref DB. Without this change we end up with sql execute errors later onDuring initial source selection, now selects the species in addition to the species_id. If the source_url is mysql:* the source and species are fed to the parser as additional args to the run method. Species and source specific queries can thus be generatedAdded Frameshiftaffy->oligoAlso skip projection of GO terms with ISS evidence code (manually projected via orthologs)gadfly dowen gradded to xref from knownxrefrelease->db_release nowdo not load GO as theses are gotten from GOParser and have linkage types from thereProperly deal with the situation when no frameshifts are found (e.g. in tetraodon).only allow 200 jobs be run at any one time. Else the coping sucks up too much resources etcconsistent column definition for analysis_id foreign keystypoAdded an entry for TIFFIN motif-finding results.modified attribute groups to be an array reffixed typochanged 'value' in attrib tables from VARCHAR(255) to TEXTmore effective duplicate filter for fetching id historydisplay_xref_id fixschema and API changes for archive stable id historyfix case sensitivity in species nameA mapper method for running exonerate jobs inline on the local machine, without using bsub. Useful for debugadded the option to choose which database get the data fromFixed bug in handling LOCAL: files; now the specified file is checksum-ed, rather than a non-existent fileFixed bug in validate_sources. Now uses the number of rows returned (rather than the row data) to validate the sourceImproved documentation for version parameter to constructor.export variable properly and use themInitialised count variables to 0 - improves debug infoUpdated version to 38Registry configuration for release 38 on staging server.missing line to set transcripts to KNOWNUses seq->alphabet for $xref->{SEQUENCE_TYPE}Committed in error. Backed out changesA simple, generic parser for FASTA sequences. Uses Bio::SeqIOfixed a bug - changed return value for create_xrefsAffy -> Oligo schema and API changes.Affy -> Oligo schema changes.this line was rm by mistakeget_all_SeqEdits now checks attributes to convert first amino acid to methionineadded attribute type to change first amino acid to methionine