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Python version of R gsalib to read GATK Report tables into pandas DataFrames

Project description

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']

License

The project is licensed under the MIT license.

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