AstrobioMike/bit: v2.0.0

A lot of changes have been made recently to group and reorganize bit commands (alongside a hefty python revamp). The changelog over several past versions should be able to help you find anything you might be looking for that's been moved. But if you're having trouble finding something you used to use, please reach out and let me know! You can post an issue on this repo or reach out to me however :)

Added

• bit by itself will print out an overview of available programs
• bit-data
  • this replaces bit-data-locations and all the database download programs with the following subcommands:
    • locations
      • check
      • set
    • get
      • ncbi-assembly-data
      • ncbi-tax-data
      • go-dbs
      • gtdb-data
      • test-data
• bit-fasta which holds subcommands as listed below
• bit-lineage which holds subcommands as listed below
• bit-kraken2 which holds subcommands as listed below
• bit-table which holds subcommands as listed below
• bit-go which holds subcommands as listed below

Changed

• several fasta-related programs have been placed as subcommands under bit-fasta
  • bit-calc-gc-per-seq and bit-calc-gc-sliding-window -> bit-fasta calc-gc
  • bit-calc-variation-in-msa -> bit-fasta calc-var-in-msa
  • bit-count-bases -> bit-fasta count
  • bit-extract-seqs by-coords -> bit-fasta extract-by-coords
  • bit-extract-seqs by-headers -> bit-fasta extract-by-headers
  • bit-extract-seqs by-primers -> bit-fasta extract-by-primers
  • bit-fasta-to-bed -> bit-fasta to-bed
  • bit-fasta-to-genbank -> bit-fasta to-genbank
  • bit-filter-fasta-by-length -> bit-fasta filter-by-length
  • bit-rename-fasta-headers -> bit-fasta modify-headers
  • bit-remove-wraps -> bit-fasta remove-wraps
    • this is moderately slower now since i took it out of shell and put in into python
    • if wanted, you can add the shell way as a function as found in this gist: https://gist.github.com/AstrobioMike/4054ce9ed84162f31c830bac03beda68
• kraken2/bracken-related programs have been placed as subcommands under bit-kraken2
  • bit-kraken2-tax-summary -> bit-kraken2 tax-summary
  • bit-kraken2-tax-plots -> bit-kraken2 tax-plots
• several table-related commands have been combined as subcommands under bit-table
  • bit-colnames -> bit-table colnames
  • bit-filter-table -> bit-table filter
  • bit-normalize-table -> bit-table normalize
  • bit-summarize-column -> bit-table summarize-column
• GO-related commands have been placed as subcommands under bit-go
  • bit-get-go-term-info -> bit-go get-term-info
  • bit-go-summarize-annotations -> bit-go summarize-annotations
  • bit-combine-go-summaries -> bit-go combine-summaries
  • bit-slim-down-go-terms -> bit-go slim-terms
  • bit-update-GO-dbs -> get-go-dbs
• database helpers for setting/checking locations has been reorganized
  • bit-data-locations -> bit-data locations
• database helpers for downloading/updating them have been reorganized
  • get-ncbi-assembly-data -> bit-data get ncbi-assembly-data
  • get-ncbi-tax-data -> bit-data get ncbi-tax-data
  • get-go-dbs -> bit-data get go-dbs
  • get-gtdb-data -> bit-data get gtdb-data
  • bit-get-test-data -> bit-data get test-data
• lineage-related helpers have been reorganized
  • bit-get-lineage-from-taxids -> bit-lineage from-taxids
  • bit-lineage-to-tsv -> bit-lineage to-tsv
• bit-filter-kofamscan-results -> bit-filter-ko-results
• bit-get-accessions-from-gtdb -> bit-get-accs-from-gtdb

Removed

• bit-version has been removed, each program has its own -v|--version flag now
• bit-dedupe-fasta-headers has been removed entirely, as it's purpose can be achieved with bit-fasta modify-headers
• bit-check-fastq-for-dup-headers removed due to only super-niche utility
• bit-parse-fastq-by-headers removed due to only niche utility, gist is here: https://gist.github.com/AstrobioMike/785265b43847e7cb10089d102573b575

Full Changelog: https://github.com/AstrobioMike/bit/compare/v1.17.0...v2.0.0