Add metadata from annotation files #227
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jpjarnoux
requested changes
Jun 3, 2024
jpjarnoux
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Jun 3, 2024
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This PR extracts information from annotation files (GBFF and GFF) and adds them as metadata to genomes and contigs in the pangenome file.
Tasks to complete:
Display metadata by default in output filesI have completely redesigned the
read_org_gbfffunction to simplify metadata extraction from GBFF files.Metadata will still no be displayed in output files by default as this behavior may lead to some error regarding the metadata separator. If the user want to display metadata in the output files, it needs to add the
--add_metadataflag as before.Note: This PR builds on the AnnotJoin branch, which has introduced several changes to annotation file parsing. Therefore, it is dependent on PR #206 and should be merged afterward.