gsalib makes it easy for Python users to analyze metrics reports created by the Broad Institute’s Genome Analysis Toolkit (GATK). The Broad provides an R library called gsalib that allows you to load GATKReport files into R for further analysis (https://gatkforums.broadinstitute.org/gatk/discussion/1244/what-is-the-gatkreport-file-format). Python gsalib is an adaptation of the R libray that allows you to load GATKReport files into Python/pandas DataFrames.
Neither the R nor Python versions of gsalib support the samtools.metrics reports created by Picard Tools. To analyze Picard reports with Python, consider using the picard.parse function in the Crimson module.
Features
Enables analysis of GATK reports with powerful pandas DataFrames and plotting
Reads GATKReport versions 0.x and 1.x
Compatible with Python >=2.7 and >=3.4
Installation
Install gsalib by running
pip install gsalib
Example
Read a report and get a table’s DataFrame:
from gsalib import GatkReport
report = GatkReport('/path/to/gsalib/test/test_v1.0_gatkreport.table')
table = report.tables['ExampleTable']
Documentation
Contribute
Issue Tracker: https://github.com/myourshaw/gsalib/issues
Source Code: https://github.com/myourshaw/gsalib
License
The project is licensed under the MIT license.
1 maintainer
Metadata
1 maintainer
Release files for gsalib 1.0.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| gsalib-1.0.6.tar.gz | 23.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gsalib-1.0.6-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 30.0 kB
Release files / gsalib-1.0.6.tar.gz
| Download URL | gsalib-1.0.6.tar.gz |
|---|---|
| Size | 23.1 kB |
| Tags | Source |
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Release files / gsalib-1.0.6-py2.py3-none-any.whl
| Download URL | gsalib-1.0.6-py2.py3-none-any.whl |
|---|---|
| Size | 7.0 kB |
| Tags | Python 2 Python 3 |
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