pydownsampler 1.0

A Python package for downsampling sequence alignment files

A Python package for downsampling sequence alignment files.

Installation

pydownsampler is available through pypi. To install, type:

pip install pydownsampler

Usage

$ pydownsampler (<file>) [-d <dcov>]
$ pydownsampler (<file>) [-d <dcov>] [-o <output>]
$ pydownsampler (<file>) [-c]
$ pydownsampler [-h] | [--help]
$ pydownsampler [-v] [--version]

Arguments and Options

Argument/ Option	Description
-h, --help	Show help message to screen.
-v, --version	Show version.
<file>	Input BAM/CRAM/SAM file
-d, --downcoverage	The coverage you want to downsample to (Required argument)
-o, --output	Output filename prefix (Optional)
-c, --coverage	Check file coverage

Examples

# option 1 (default):
$ pydownsampler input.bam -d 10
In the example above, the file 'input.bam' will be downsampled to 10X coverage. The output filename will be 'input.Downsampled10X.bam'.

# option 2 (optional):
$ pydownsampler input.bam -d 10 -o downsampled

# check coverage of a BAM/CRAM/SAM file
$ pydownsampler input.bam -c

Authors

Lindokuhle Nkambule

Scott Hazelhurst

License

pydownsampler is generously distributed under The MIT License