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v1.5.8

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@dmacguigan dmacguigan released this 29 Sep 17:18
· 3 commits to main since this release
1.5.8
c0b93e4

New Features

  • NCBI BioSample metadata. Samples can now be linked to an NCBI BioSample, directly or through an SRA accession (SRR, ERR, DRR, SRX, or SRS), with mapping_biosample at setup, fetch_biosample(), or the new NCBI tab in the sample metadata viewer. MitoPilot stores every BioSample attribute plus the linked BioProjects, adds NCBI to the Compare tab and the export conflict warning, and offers GenBank-ready ncbi_* fields at export. See Sample metadata.
  • Follow links between GEOME, GBIF, and NCBI. With link_sources = TRUE at setup (or Follow links between databases in the sample metadata viewer), each fetched record is read for IDs of the other databases, and missing ones are added and fetched: BioSample to GEOME tissue and Smithsonian voucher, GEOME to BioSample and voucher, GBIF to BioSample. Other museums' vouchers are matched to GBIF by catalog number, and only linked when exactly one specimen of the right species is found. Your own IDs are never replaced, and every linked ID shows where it came from.
  • Remove fetched metadata. Remove fetched data... in the sample metadata viewer, or remove_metadata(), deletes fetched GEOME, GBIF, or NCBI records for one sample or all. Mapping-file columns and the IDs you supplied are always kept.
  • Curation ruleset browser tweaks. Each clade now shows a representative image from Wikipedia, credited to its author and license with links to the Wikimedia Commons file

Bug Fixes

  • Assemblies keep their N gaps after annotation. Bases with no read coverage, mostly the runs of N that map-to-reference assembly produces where no reads map, were dropped from the saved sequence when annotation finished. Gene coordinates stayed on the full sequence, so every feature after the first dropped run of Ns had incorrect annotation coordinates. The coverage table now has one row per base (depth 0 over gaps), the saved sequence comes from the curated assembly the annotations were built on, and annotation stops with an error instead of saving a sequence that does not match its coverage. Coverage files from earlier versions are completed automatically when annotation runs, so Assemble does not need to be re-run. Re-run annotation on affected samples and re-export them.

Note
To update older MitoPilot projects, please run MitoPilot::backwards_compatibility(). This will add any missing fields to the SQL database and attempt to update the Docker/Singularity container version in your project .config file.

Full Changelog: 1.5.7...1.5.8

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