AstrobioMike/bit: v1.15.0

Added

• bit-mutate-seqs now has a tunable parameter for transitions/transversions
• bit-extract-seqs
  • added by-headers subcommand (this replaces bit-parse-fasta-by-headers)
  • by-coords subcommand replaces bit-extract-seqs-by-coords
• bit-genbank which has subcommmands for all genbank helpers
  • to-fasta replaces bit-genbank-to-fasta
  • to-AA-seqs replaces bit-genbank-to-AA-seqs
  • to-cds-seqs
  • to-cds-tsv replaces bit-genbank-to-cds-table

Changed

• removed bit-figshare-upload, that is now just stored as a gist here: https://gist.github.com/AstrobioMike/9f86931747357ae8949f715145c5eec4
• removed bit-locus-clean-slate, that is now just stored as a gist here: https://gist.github.com/AstrobioMike/17324583568b051cd3b190cf4767b524
• moved many imports from top of cli modules until they are needed to increase snappiness when just doing things like trying to view the help menu
• bit-summarize-column no longer has an -i flag, it expects the input table/file to be given as a positional argument
• bit-count-bases can now take STDIN
• bit-normalize-table modularized and tests added
• bit-parse-fasta-by-headers has been removed and replaced with bit-extract-seqs by-headers
• bit-extract-seqs-by-coords has been removed and replaced with bit-extract-seqs by-coords
• bit-filter-seqs-by-length has been renamed to bit-filter-fasta-by-length
• bit-genbank-to-fasta has been removed and replaced with bit-genbank to-fasta
• bit-genbank-to-AA-seqs has been removed and replaced with bit-genbank to-AA-seqs
• bit-genbank-to-cds-table has been removed and replaced with bit-genbank to-cds-tsv
• bit-genbank-to-clean-slate has been removed and replaced with bit-genbank clean-slate
• moved bit-GL-combine-contig-tax-tables and bit-GL-combine-KO-and-tax-tables from the primary bit package into the metagenomics-wf scripts
• bit-get-test-data metagenome pulls a smaller, super simple, single-sample dataset I'm hosting on github now rather than figshare