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Refactor organism import/export; consider GAF source

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@puethe puethe released this 26 Feb 15:55
· 40 commits to master since this release
v0.2.8
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Learn about vigilant mode.

  • rename 'chado extract genedb_products' to 'chado extract gene_products'

  • 'chado import gff': do not insert chromosomes into featureloc table, since this is redundant information

  • 'chado import gff': save attribute 'colour' in featureprop table

  • 'chado import gaf': extract the information from column 15 of the GAF file ("Assigned_by") and save it in the feature_cvtermprop table with appropriate key

  • 'chado export gaf': extract information for column 15 of the GAF file ("Assigned_by") from the feature_cvtermprop table, and use the database authority specified with flag '-A' as fallback

  • 'chado import essentials': import CV terms 'assigned_by', 'colour' and 'version' into the database

  • drop column 'version' from organism table

  • completely refactor organism insert/delete/select

  • 'chado insert organism': new optional flags '--genome_version', '--taxon_id' and '--wikidata_id'; specified values are imported into the organismprop / organism_dbxref tables

  • 'chado extract organisms': query tables organism, organismprop and organism_dbxref to extract all available information on the organism, including genome version, taxon ID and Wikidata ID (if given).

  • 'chado export fasta': add feature names to FASTA header, if present

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