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EFS Parser

Documentation Status

epivizFileParser

Parse and Query Genomic File Formats

Description

EFS parser provides parsers and utility methods to read and query commonly used genomic file formats. The results of the query are transformed into a Pandas DataFrame. This allows users to take advantage of many of the visual and analysis packages in the pandas/numpy ecosystem.

Explore the docs

Class information

A new parser for a file format can be added to the package. The minimum skeleton is available in the skeleton directory

Developer Notes

This project has been set up using PyScaffold 4. For details and usage information on PyScaffold see https://pyscaffold.org/.

use a virtualenv for testing & development. To setup run the following commands from the project directory

virtualenv env --python=python3
source env/bin/activate # (activate.fish if using the fish-shell)
pip install -r requirements.txt

# to deactivate virtualenv
deactivate
  1. Test - `python setup.py test`
  2. Docs - `python setup.py docs`
  3. Build
    • source distribution `python setup.py sdist`
    • binary distribution `python setup.py bdist`
    • wheel distribution `python setup.py bdist_wheel`

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Parse and Query Genomic File Formats.

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