pydownsampler 1.0
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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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