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توضیحات

A Python package for working with Bactopia

ویژگی	مقدار
سیستم عامل	-
نام فایل	bactopia-1.0.2
نام	bactopia
نسخه کتابخانه	1.0.2
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Robert A. Petit III
ایمیل نویسنده	robbie.petit@gmail.com
آدرس صفحه اصلی	https://bactopia.github.io/
آدرس اینترنتی	https://pypi.org/project/bactopia/
مجوز	MIT

[![Gitpod ready-to-code](https://img.shields.io/badge/Gitpod-ready--to--code-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/bactopia/bactopia-py) ![Bactopia Logo](https://raw.githubusercontent.com/bactopia/bactopia/master/data/bactopia-logo.png) # bactopia-py A Python package for working with [Bactopia](https://bactopia.github.io/) ## 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` ```{bash} 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` ```{bash} 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` ```{bash} 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` ```{bash} 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` ```{bash} 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` ```{bash} 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](https://github.com/bactopia/bactopia/issues). # License [MIT License](https://raw.githubusercontent.com/bactopia/bactopia/master/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](https://twitter.com/rpetit3)

نیازمندی

مقدار	نام
>=23.2,<24.0	executor
>=1.5.3,<2.0.0	pandas
>=1.4.2,<2.0.0	pysradb
>=2.28.2,<3.0.0	requests
>=13.3.1,<14.0.0	rich
>=1.6.1,<2.0.0	rich-click

زبان مورد نیاز

مقدار	نام
>=3.8.0,<4.0.0	Python

نحوه نصب

نصب پکیج whl bactopia-1.0.2:

pip install bactopia-1.0.2.whl

نصب پکیج tar.gz bactopia-1.0.2:

pip install bactopia-1.0.2.tar.gz