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Refactor ORF main type, update entire writting API and other general changes #23

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merged 42 commits into from
Jan 10, 2024

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@camilogarciabotero camilogarciabotero commented Jan 9, 2024

This PR creates important changes to the API including:

  • A more stable ORF type that asserts for incorrect ORFs.
  • Extended Base.getindex method to better handle ORF enabling: seq[orf] regardless of the ORF strand.
  • The write_* API is much more stable and its been rewriten to handle IOStreams and IOBuffers as well.
  • The new record_orfs_fna and record_orfs_faa methods intearact with the FASTX interface.
  • Codebase has been reduced. Direct String manipulation is not enabled for findorfs and get_* methods.
  • Docstrings have been updated following method updates.
  • Better tests and now Aqua.jl is used for several tests as well.

Still some things to do:

  • Create a new documentation section to describe write_orfs* API
  • Update CHANGELOG.md using the bulletpoints of this PR.
  • Update Project.toml to bump version.
  • Add the Aqua badge.

@camilogarciabotero camilogarciabotero changed the title Refactor gene structs and update types Refactor ORF main type, update entire writting API and other general changes Jan 10, 2024
@camilogarciabotero camilogarciabotero merged commit c0105b8 into main Jan 10, 2024
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