v1.8.63

• updating bit-get-accessions-from-GTDB
  • updated links so they match new changes in GTDB
    • *metadata.tar.gz file suffixes were changed to *metadata.tsv.gz
  • improved formatting of output filenames when doing a species search (so spaces are replaces with dashes)

v1.8.62

• updating bit-combine-bracken-and-add-lineage to accept a user-specific taxonkit db directory rather than the default ~/.taxonkit location, thanks to contribution from @sterrettJD (#16)

v1.8.61

• updating bit-dl-ncbi-assemblies to enable downloading nucleotide cds files (*_cds_from_genomic.fna.gz, based on input format argument of "nt_cds")

v1.8.60

• bit-kraken2-to-taxon-summaries

  • updated to use pandas concat instead of append, as append has become deprecated from v2+ (https://stackoverflow.com/a/75956237)
  • added test data (test-data/kraken-example-output.tsv)

• not managed here, but from v1.8.60 on, the conda install requires pandas v2+

v1.8.57

• adding flag to bit-lineage-to-tsv that will make arbitrary taxids useful for other helper programs

v1.8.56

• adding bit-lineage-to-tsv and shebang fix 🤦‍♂️

v1.8.55

• adding bit-lineage-to-tsv

v1.8.54

• moved scripts to bit sub-directory so not cluttering up repo home page
• added bit-data-locations (repurposed from GToTree) to manage any ref data locations
• added helper-bit-check-or-setup-GTDB-files.py
• started stub-bit-GTDB-tax-to-NCBI-tax, but with other avenues not sure if i'm going to finish it. For now leaving as a stub with a message if called about another way to do this with sourmash 👍

v1.8.53

• updating bit-get-accessions-from-GTDB 41adaa0
  • download was failing due to the GTDB switch from 122 to 53 marker-genes for archaea (https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/RELEASE_NOTES)

v1.8.52

• fix to recent bug introduced to bit-dl-ncbi-assemblies
  • was an indentation problem in helper-bit-parse-assembly-summary-file.py)