bbmapy 0.0.56

A Python wrapper for BBTools

bbmapy

A Python wrapper for BBTools. Current version of bbmapy is v39.59.

Installation

conda install -c bioconda -c conda-forge bbmapy # not yet available on conda-forge

Also available on pip (but does not ensure java is available):

pip install bbmapy

Usage

bbmapy let's you call bbtools stuff from python. To the shell only one CLI is available:

• bbmapy-test: Run tests to verify installation

Example

from bbmapy import bbmap

# Run bbmap.sh
bbmap.bbmap(
    in1="reads1.fastq",
    in2="reads2.fastq",
    out="mapped.sam",
    ref="reference.fasta"
)

Dependencies

• Python >= 3.9
• rich
• install-jdk (this will be used to install a JRE if needed)

Usage

After installation, you can use bbmapy in your Python scripts like this:

from bbmapy import bbduk

# Basic usage
bbduk(
    in_file="input.fastq",
    out="output.fastq",
    ktrim="r",
    k="23",
    mink="11",
    hdist="1",
    tbo=True,
    tpe=True,
    minlen="45",
    ref="adapters",
    ftm="5",
    maq="6",
    maxns="1",
    ordered=True,
    threads="4",
    overwrite="t",
    stats="stats.txt"
)

Using Java flags alongside other arguments

bbduk(
    Xmx="2g",  # Set maximum heap size
    da=True,   # Enable assertions
    eoom=True, # Enable out-of-memory termination
    in_file="input.fastq",
    out="output.fastq",
    ktrim="r",
    k="23"
)

To capture output

You need to set capture_output=True in the function call, AND out="stdout.fastq" (or any other file format you like).

stdout, stderr = bbduk(
    capture_output=True,
    Xmx="2g",
    in_file="input.fastq",
    out="stdout.fastq",
    # ... other parameters ...
)

Getting java executable

Can be a pain, see this PR discussion.
bioconda's recipes that require java will usually bring a really bloated set of stuff. not good. way too much useless bandwidth (I see no reason that getting bbmap would require alsa).
But pip and bioconda recipies allow using other pip and conda recipes. Good. A workaround - adding a custom function that recognizes the os + arch and fetches during install or test.
Technically - this does not count as preloading a binary/executable. The actual JRE is tiny, and getting it can be done via install-jdk.

tl;dr: after installing from pypi (via pip/uv/pixi)

bbmapy-ensure-java

Notes:

• in can be a protected word in python and other code, it is replaced by in_file in function calls. in1, in2 are still valid.
• Java flags (such as Xmx, Xms, da, ea, eoom) are automatically recognized and handled appropriately. Include them in your function calls just like any other argument.
• the capture_output argument might be switched (stderr --> out and vice verse).
• Flags (i.e. argument that do not take value in the OG bbmap version) are set with Boolean values. e.g.:

flag : True

Not to be mistaken for lower case, fouble qouted "true" and "false" for boolian arguments to be passed to bbtools, e.g.:

argument : "true"

Citation

BBMerge manuscript: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185056 Please cite this paper if you use bbmap in your work.

License

This project is only a wrapper, please see the actual bbtools repository for (license)[https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/license.txt] etc.
Neither the developers of bbtools nor of bbmapy take any responsibility for how you use this code. All accountability is on you.

Acknowledgments

This project only (crudely) wraps BBTools (a.k.a bbmap), which is developed by Brian Bushnell.
If you use bbmapy and things don't quite work like you'd like, don't expect the developer of bbmap to help you with this whacky python wrapper.
Please see the BBTools website for more information about the underlying tools.

to build and upload to pypi

rm -rf dist build egg-info
pixi run python bbmapy/update.py # fetch latest version of bbtools and update version in pyproject.toml
rm bbmapy/vendor/bbmap/pytools -rf # remove the pytools folder
pixi run pip install --upgrade build twine
pixi run python -m build
pixi run twine upload dist/*