Python version of R gsalib to read GATK Report tables into pandas DataFrames
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.
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
Install gsalib by running
pip install gsalib
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']
Issue Tracker: https://github.com/myourshaw/gsalib/issues
Source Code: https://github.com/myourshaw/gsalib
The project is licensed under the MIT license.
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