Description:
pydownsampler 1.0
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
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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