bbmapy 0.0.41

A Python wrapper for BBTools

bbmapy

A Python wrapper for BBTools.
Current BBMap version: 0.0.41

Installation

1. Lazy way - Clone this repository, download bbmap, and install the package:

   git clone https://github.com/urineri/bbmapy.git
   cd bbmapy
   cd vendor
   rm bb* -rf
   wget https://sourceforge.net/projects/bbmap/files/latest/download -O bbtools.tar.gz
   tar -xf bbtools.tar.gz
   cd ..
   pip install -e .
   generate-bbmapy-commands
   

   The above should be automatically done or just not needed if you are installing from pip (pypi)

2. Unlazy way - is commented out below this line, that's how much it isn't suggested.

Dependencies

• Java
• BBmap (the above steps should download it to the vendor subdirectory...).
  If you rather this to use your own bbmap etc, go to the base.py script and comment out line 51, then uncomment line 52.
• rich (for pretty printing)

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 ...
)

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.
If Please see the BBTools website for more information about the underlying tools.