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

Metagenomics workflow v1.0.3

• CAT was having trouble downloading its DB, so added -k to curl command
• moved bit-GL-combine-contig-tax-tables and bit-GL-combine-KO-and-tax-tables from bit package into workflow scripts

v1.14.0

Added

• to bit-cov-analyzer
  • progress updates while running
  • zero-coverage region outputs now also generated
  • output region tsvs now have a "low_complexity" column that holds True or False
    • this is based on:
      • low_complexity = True if: unique 3-mers / all-possible-3mers <= 0.4
• bit-extract-seqs
  • enables pulling out target seqs from a fasta by bed file or specified primers via subcommands
• to bit-gen-reads
  • --fragment-size-range option added, defaults to 10% of fragment size

Changed

• bit-cov-analyzer
  • -s | --sliding-window-size changed to -w | --window-size, and -S | --step-size changed to -s | --step-size (lower-case)
  • default window size change from 50 to 100, and default step size changed from 10 to 20
  • drastic improvements to efficiency when working with large genomes (e.g., 3GB)
  • histogram of coverages no longer plotted by default, only done now when adding the --write-window-stats flag
  • no longer produces window-coverage-overview.txt as all of that info is captured within window-coverage-overview.tsv
• bit-get-mapped-reads-pid
  • minor improvements to efficiency
• bit-get-cov-stats
  • improvements to efficiency
  • now also reports median percent id of mapped reads per ref and per contig (when provided an input bam file)
• bit-summarize-assembly
  • adds commas when printing stats to terminal for readability
• bit-extract-seqs-by-coords is now combined into bit-extract-seqs
• bit-gen-reads
  • now has a --fragment-size-range that defaults to 10% of fragment size
  • by default will not include regions with Ns in generated reads, add --include-Ns to allow that

v1.13.15

Changed

• bit-assemble
  • the threads parameter is now passed to bbnorm and fastp (if run) in addition to the assemblers
• bit-gen-reads
  • --type long will no longer preferentially start reads at position 0 if the requested read size is larger than the contig; now it will start randomly and just produce a read that ends where the contig ends (unless --circularize is added)
• bit-cov-analyzer
  • no longer writes out individual window stats by default (to save spacetime), it needs to be turned on with the --write-window-stats now if wanted

Full Changelog: v1.13.14...v1.13.15

v1.13.14

Fixed

• bit-gen-reads previously may have by chance created reads with identical headers (since only coordinates were being added), now there is also a counter to prevent this

Full Changelog: v1.13.13...v1.13.14

SRA download workflow v1.1.1

• fix duplication of "fastq" in output filenames

v1.13.13

Added

• to bit-gen-reads
  • added single-end and long-read capabilities (through --type argument now, see Changed below)
  • single can be used up to any size, but if specifying --long, it will also generate reads with lengths spanning a range around the specified read size (50% by default)
• to bit-calc-variation-in-msa
  • 3Di as an option for --type

Changed

• bit-gen-reads
  • now has --type flag for paired-end, single-end, or long (paired-end still by default)
  • did more work than it's worth to ensure the exact number of requested reads are always returned
• bit-calc-variation-in-msa
  • --gaps-treatment changed to "include" by default

Full Changelog: v1.13.12...v1.13.13

v1.13.12

Added

• bit-add-insertion

Full Changelog: v1.13.11...v1.13.12

v1.13.11

Changed

• bit-update-ncbi-taxonomy replaced with get-ncbi-tax-data (prior still retained for now)
• dropped bit-calc
  • if you are the one other person that ever used this and you want it back, you can add this to your ~/.bashrc: bit-calc () { awk "BEGIN { print $1 }"; } :)
• modified bit-colnames to try to autodetect delimeter

Fixed

• added back in setup.py glob portion needed for scripts not fully integrated into python-packaging yet

v1.13.10

Changed

• bit-get-cov-stats
  • the --include-non-primary flag now in addition to calculating percent ID including supplemental and secondary alignments also runs mosdepth with --flag 1540
• bit-dl-ncbi-assemblies
  • in python now instead of bash (i hope this doesn't hinder performance too much...)
  • default concurrent downloads is 10 now instead of 1
  • default format is fasta now instead of gbk
  • downloads only happen in http now, no more ftp, so the -P flag to specify http has been removed
  • added optional output dir
• no longer keeping stubs in scripts/, instead keeping a ton of entry points in pyproject.toml
• bit-filter-seqs-by-length renamed to bit-filter-fasta-by-length to be more specific (prior still retained for now)

Full Changelog: v1.13.9...v1.13.10