A Python package for working with Bactopia
Project description
bactopia-py
A Python package for working with Bactopia
Bactopia Subcommands
There are many subcommands available in Bactopia. Here is a brief description of each command:
| Command | Description |
|---|---|
bactopia-citations |
Print out tools and citations used throughout Bactopia |
bactopia-datasets |
Download optional datasets to supplement your analyses with Bactopia |
bactopia-download |
Builds Bactopia environments for use with Nextflow. |
bactopia-prepare |
Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia |
bactopia-search |
Query against ENA and SRA for public accessions to process with Bactopia |
bactopia-summary |
Generate a summary table from the Bactopia results. |
Below is the --help output for each subcommand.
bactopia-citations
Usage: bactopia-citations [OPTIONS]
Print out tools and citations used throughout Bactopia
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --version -V Show the version and exit. │
│ * --bactopia-path -b TEXT Directory where Bactopia repository is stored │
│ [required] │
│ --name -n TEXT Only print citation matching a given name │
│ --plain-text -p Disable rich formatting │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bactopia-datasets
Usage: bactopia-datasets [OPTIONS] [UNKNOWN]...
Download optional datasets to supplement your analyses with Bactopia
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --bactopia-path TEXT Directory where Bactopia repository is stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Download Related Options ───────────────────────────────────────────────────────────╮
│ --datasets_cache TEXT Base directory to download datasets to (Defaults to env │
│ variable BACTOPIA_CACHEDIR, a subfolder called datasets │
│ will be created) │
│ [default: ${HOME}/.bactopia] │
│ --force Force overwrite of existing pre-built environments. │
│ --max_retry INTEGER Maximum times to attempt creating Conda environment. │
│ (Default: 3) │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --verbose Print debug related text. │
│ --silent Only critical errors will be printed. │
│ --version Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bactopia-download
Usage: bactopia-download [OPTIONS] [UNKNOWN]...
Builds Bactopia environments for use with Nextflow.
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --bactopia-path TEXT Directory where Bactopia results are stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Build Related Options ──────────────────────────────────────────────────────────────╮
│ --envtype [conda|docker|singularity| The type of environment to │
│ all] build. │
│ [default: conda] │
│ --wf TEXT Build a environment for a │
│ the given workflow │
│ [default: bactopia] │
│ --condadir TEXT Directory to create Conda │
│ environments │
│ (NXF_CONDA_CACHEDIR env │
│ variable takes precedence) │
│ --use_conda Use Conda for building │
│ Conda environments instead │
│ of Mamba │
│ --singularity_cache TEXT Directory to download │
│ Singularity images │
│ (NXF_SINGULARITY_CACHEDIR │
│ env variable takes │
│ precedence) │
│ --singularity_pull_docker… Force conversion of Docker │
│ containers, instead │
│ downloading Singularity │
│ images directly │
│ --force_rebuild Force overwrite of │
│ existing pre-built │
│ environments. │
│ --max_retry INTEGER Maximum times to attempt │
│ creating Conda │
│ environment. (Default: 3) │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --verbose Print debug related text. │
│ --silent Only critical errors will be printed. │
│ --version Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --build-all Builds all environments for Bactopia workflows │
│ --build-nfcore Builds all nf-core related environments │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bactopia-prepare
Usage: bactopia-prepare [OPTIONS]
Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --path -p TEXT Directory where FASTQ files are stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Matching Options ───────────────────────────────────────────────────────────────────╮
│ --assembly-ext -a TEXT Extension of the FASTA assemblies [default: .fna.gz] │
│ --fastq-ext -f TEXT Extension of the FASTQs [default: .fastq.gz] │
│ --fastq-separator TEXT Split FASTQ name on the last occurrence of the │
│ separator │
│ [default: _] │
│ --pe1-pattern TEXT Designates difference first set of paired-end reads │
│ [default: [Aa]|[Rr]1|1] │
│ --pe2-pattern TEXT Designates difference second set of paired-end reads │
│ [default: [Bb]|[Rr]2|2] │
│ --merge Flag samples with multiple read sets to be merged by │
│ Bactopia │
│ --ont Single-end reads should be treated as Oxford Nanopore │
│ reads │
│ --recursive -r Directories will be traversed recursively │
│ --prefix TEXT Prefix to add to the path │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Sample Information Options ─────────────────────────────────────────────────────────╮
│ --metadata TEXT Metadata per sample with genome size and species │
│ information │
│ --genome-size -gsize INTEGER Genome size to use for all samples │
│ --species -s TEXT Species to use for all samples (If available, can be │
│ used to determine genome size) │
│ --taxid TEXT Use the genome size of the Taxon ID for all samples │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --examples Print example usage │
│ --verbose Increase the verbosity of output │
│ --silent Only critical errors will be printed │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bactopia-search
Usage: bactopia-search [OPTIONS]
Query against ENA and SRA for public accessions to process with Bactopia
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --query -q TEXT Taxon ID or Study, BioSample, or Run accession (can also be │
│ comma separated or a file of accessions) │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Query Options ──────────────────────────────────────────────────────────────────────╮
│ --exact-taxon Exclude Taxon ID descendants │
│ --limit -l INTEGER Maximum number of results (per query) to return │
│ [default: 1000000] │
│ --accession-limit -al INTEGER Maximum number of accessions to query at once │
│ [default: 5000] │
│ --biosample-subset INTEGER If a BioSample has multiple Experiments, maximum │
│ number to randomly select (0 = disabled) │
│ [default: 0] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Filtering Options ──────────────────────────────────────────────────────────────────╮
│ --min-base-count -mbc INTEGER Filters samples based on minimum base pair count │
│ (0 = disabled) │
│ [default: 0] │
│ --min-read-length -mrl INTEGER Filters samples based on minimum mean read length │
│ (0 = disabled) │
│ [default: 0] │
│ --min-coverage -mc INTEGER Filter samples based on minimum coverage (requires │
│ --genome_size, 0 = disabled) │
│ [default: 0] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --genome-size -gsize INTEGER Genome size to be used for all samples, and for │
│ calculating min coverage │
│ [default: 0] │
│ --outdir -o TEXT Directory to write output [default: ./] │
│ --prefix -p TEXT Prefix to use for output file names │
│ [default: bactopia] │
│ --force Overwrite existing reports │
│ --verbose Increase the verbosity of output │
│ --silent Only critical errors will be printed │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
bactopia-summary
Usage: bactopia-summary [OPTIONS]
Generate a summary table from the Bactopia results.
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --bactopia-path -b TEXT Directory where Bactopia results are stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Gold Cutoffs ───────────────────────────────────────────────────────────────────────╮
│ --gold-coverage -gcov INTEGER Minimum amount of coverage required for Gold │
│ status │
│ [default: 100] │
│ --gold-quality -gqual INTEGER Minimum per-read mean quality score required │
│ for Gold status │
│ [default: 30] │
│ --gold-read-length -glen INTEGER Minimum mean read length required for Gold │
│ status │
│ [default: 95] │
│ --gold-contigs -gcontigs INTEGER Maximum contig count required for Gold │
│ status │
│ [default: 100] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Silver Cutoffs ─────────────────────────────────────────────────────────────────────╮
│ --silver-coverage -scov INTEGER Minimum amount of coverage required for │
│ Silver status │
│ [default: 50] │
│ --silver-quality -squal INTEGER Minimum per-read mean quality score │
│ required for Silver status │
│ [default: 20] │
│ --silver-read-length -slen INTEGER Minimum mean read length required for │
│ Silver status │
│ [default: 75] │
│ --silver-contigs -scontigs INTEGER Maximum contig count required for Silver │
│ status │
│ [default: 200] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Fail Cutoffs ───────────────────────────────────────────────────────────────────────╮
│ --min-coverage -mincov INTEGER Minimum amount of coverage required to pass │
│ [default: 20] │
│ --min-quality -minqual INTEGER Minimum per-read mean quality score │
│ required to pass │
│ [default: 12] │
│ --min-read-length -minlen INTEGER Minimum mean read length required to pass │
│ [default: 49] │
│ --max-contigs INTEGER Maximum contig count required to pass │
│ [default: 500] │
│ --min-assembled-size INTEGER Minimum assembled genome size │
│ --max-assembled-size INTEGER Maximum assembled genome size │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --outdir -o PATH Directory to write output [default: ./] │
│ --prefix -p TEXT Prefix to use for output files [default: bactopia] │
│ --force Overwrite existing reports │
│ --verbose Increase the verbosity of output │
│ --silent Only critical errors will be printed │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
Feedback
Your feedback is very valuable! If you run into any issues using Bactopia, have questions, or have some ideas to improve Bactopia, I highly encourage you to submit it to the Issue Tracker.
License
Citation
Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems. 5 (2020), https://doi.org/10.1128/mSystems.00190-20.
Author
- Robert A. Petit III
- Twitter: @rpetit3
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