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CHANGELOG.md

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v1.0.2 [2023-11-03]

  • Make constellation determination more robust with partial, case-insensitive matching
  • Correct H3 motif by adding missing site (159)
  • Fix fetch-unclassified-swine.rq to include GISAID strains

v1.0.1 [2022-02-16]

  • Fix dependency handling

v1.0.0 [2022-02-11]

My final release

  • Refactor with mypy
  • Many bug fixes

v0.13.2 [2021-12-23]

  • Fix yet another bug

v0.13.1 [2021-12-22]

  • Fix bug in prep unpublished

v0.13.0 [2021-12-17]

  • Add version argument
  • Make pulling of tag data optional
  • Write failed genbank parses to a log file
  • Only skip if cached genbank ttl file has size greater than 0

v0.12.1 [2021-12-16]

  • Bug fixes

v0.12.0 [2021-12-15]

  • Extended documentation in README
  • Do not include gisaid data by default (replace --no-gisaid flag in octofludb pull with --include-gisaid)
  • Fix read error in octofludb prep fasta
  • Remove the octofludb make subcommand
    • moved octofludb make masterlist to octofludb report masterlist
    • removed const and subtypes, just run SPARQL queries instead

v0.11.0 [2021-11-08]

  • Add motif generation to pull
  • Add options to limit what data is updated with pull
  • Add deletion commands

v0.10.1 [2021-10-19]

  • Bug fixes in octoFLU wrapper

v0.10.0 [2021-10-06]

  • Move imports to location of use (speeds usage mesages)
  • Remove unused clean command
  • Bug fixes

v0.9.0 [2021-09-24]

  • Remove script folder and all bash scripting
  • Add pull subcommand for updating the database
  • Add classify subcommand as a wrapper around octoFLU
  • Add a config file that contains links to all data and the octoFLU reference

v0.8.0 [2021-08-12]

  • Fix subtype generation
  • Fix bugs in init
  • Add report monthly --context to pull sequences for comparisons
  • Add support for the the SPARQL CONSTRUCT command
  • Do not generate "unknown" triples

v0.7.0 [2021-04-12]

  • Add monthly report generator (used for WGS selections)
  • Standardize subtype handling (see runtest get_subtypes tests)
  • Replace "VTX98" with "LAIV" in internal gene parser
  • Add header to octofludb make const output
  • Add handlers for working with unpublished data
  • Convert internal gene clades to uppercase

v0.6.0

  • Add options for updating a certain number of months to update_gb
  • Add maxyear option to update_gb
  • Fix bug in update_gb that prevented updating of pre-2000 data
  • Fix handling of segment subtypes
  • Determine strain subtype using octoFLU info

v0.5.1

  • in update_gb - work backwards through months, not just years

v0.5.0

  • new subcommands:

    • update_gb: add missing genbank entries
    • const: generate constellations for all swine strains
    • masterlist: generate the A0 masterlist used in NADC quarterly/annual reports and octoflushow

  • cleaner strain name parsing:

    • require two forward slashes
    • remove parenthesis/bracket terms, for example: "A/wherever/2020 (H1N1)" --> "A/whereever/2020"
    • replace space with underscores, for example: "A/South Dakota/2020" --> ""A/South_Dakota/2020""

  • improved data extraction from genbank records

    • link parental strains to genbank segment records
    • link strain info to the parental strain, including:
      • host - with new cleaning
      • country - with new cleaning
      • A0 numbers - for USA strains
      • states - for USA strains
      • collection date - as string literal
    • fix incorrect (s, length, locus) link
    • convert create_date from string literal to date
    • convert update_date from string literal to date
    • convert length from string literal to integer

v0.4.0

  • Update patterns for global clades
    • allow "Other-Equine" and such
    • allow lowercase letters after "3.XXXX."

v0.3.0

  • Add first recipe - a subcommand for getting all constellations
  • Allow the constellation MIXED and allow X for unknown clades

v0.2.0

  • Change default repo name to "octofludb"
  • Replace docopt with argparse
  • Renamed all load_* commands to mk_*. The commands are not "loading" data into the database but only creating turtle files
  • Change name to octofludb
  • Add query and upload subcommands
  • Remove sameAs relationship between Strain tokens. This relationship was equating strain names (e.g. A/Michigan/288/2019) with epiflu isolate ids (e.g., EPI_ISL_381463). However, one strain name may be shared by multiple epiflu isloate ids, so the sameAs relationship is incorrect.

v0.1.0

Everything up to the point where the name changed from d79 to octofludb