AstrobioMike/bit: v1.17.0

Added

• bit-itol with subcommands for
  • binary-dataset
  • colorstrip
  • map
  • text-dataset

Changed

• bit-gen-reads fragment size and long-read read lengths are now pulled from a normal distribution rather than uniform
• bit-get-mapped-reads-pid has been renamed to just bit-mapped-reads-pid
• bit-colnames can also just accept stdin now
• bit-gen-kraken2-tax-plots changed to bit-kraken2-tax-plots
• bit-kraken2-to-taxon-summaries changed to bit-kraken2-tax-summary
• bit-combine-kraken2-taxon-summaries
  • changed to bit-kraken2-combine-tax-summaries
  • -n, --sample-names now taken as a space-delimited list instead of a comma-delimited list (to match how input files are taken)
• bit-kraken2-to-taxon-summaries has been replaced with bit-kraken2-tax-summary
• bit-kraken2-combine-tax-summaries removed, bit-kraken2-tax-summary automatically does this now, and can take multiple input reports
• bit-combine-bracken-and-add-lineage removed, bracken reports are also done by bit-kraken2-tax-summary now
  • as a result of this, like the lineage-building from kraken2 reports, this builds them based on what's in the report rather than based on taxids and new lookups. This ensures the output lineages will match the state of the taxonomy when kraken2/bracken was run (as it's only pulling from the report itself)
• bit-gen-iToL-binary-dataset replaced with bit-itol binary-dataset
• bit-gen-iToL-colorstrip replaced with bit-itol colorstrip
• bit-gen-iToL-map replaced with bit-itol map
• bit-gen-iToL-text-dataset replaced with bit-itol text-dataset
• removed bit-reorder-fasta, that is now stored as a gist here: https://gist.github.com/AstrobioMike/6b91769ad13305ebd4779873afa9aa1f
• removed bit-prot-acc-to-taxid, that is now stored as a gist here: https://gist.github.com/AstrobioMike/2cc5fd147aa28c2b793c7c664502734d
• bit-get-accessions-from-GTDB has had the --RefSeq-representatives-only flag changed to --RefSeq-reference-genomes-only to match the NCBI change (https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/#reference_genomes)

Fixed

• bit-summarize-assembly
  • would previously fail if the genome(s) trying to be summarized were in a read-only location, that shouldn't happen anymore

NOTE

bit is undergoing some changes, and some programs are being renamed and/or grouped into single programs with subcommands for organizational purposes. If you can't find something you are looking for, check in the CHANGELOG.md, or post an issue asking :)

P.S. - Sorry for doing this without a major version increment. I started small and it kind of spiraled, and now I'm waiting until it's all done ¯_(ツ)_/¯