A Python package for downsampling sequence alignment files.
Installation
pydownsampler is available through pypi. To install, type:
pip install pydownsamplerUsage
$ 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 -cLicense
pydownsampler is generously distributed under The MIT License
1 maintainer
Release files for pydownsampler 1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pydownsampler-1.0.tar.gz | 4.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pydownsampler-1.0-py2-none-any.whl | Python 2 | none | any | Details |
Total release size: 10.0 kB
Release files / pydownsampler-1.0.tar.gz
| Download URL | pydownsampler-1.0.tar.gz |
|---|---|
| Size | 4.3 kB |
| Tags | Source |
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Release files / pydownsampler-1.0-py2-none-any.whl
| Download URL | pydownsampler-1.0-py2-none-any.whl |
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| Size | 5.7 kB |
| Tags | Python 2 |
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