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Microbial pan-GWAS using the output from Roary

Project Description

Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. It reports a list of genes sorted by strength of association per trait.

Dependencies

  • Python (Tested with versions 2.7 and 3.5)
  • SciPy (Tested with versions 0.16, 0.17, 0.18)

If you supply custom trees (Optional)

  • ete3
  • six

Note that ete3 and six are not automatically installed. You can do pip install ete3 six to get them

Using the GUI (Optional)

  • Tkinter/ttk

Tkinter/ttk is already part of most python distributions. If you lack it consider getting Homebrew/Linuxbrew and running brew install python –with-tcl-tk

Installation

The easiest way to install Scoary is through the pip package manager:

pip install scoary

Usage

scoary -g <gene_presence_absence.csv> -t <traits.csv>

Documentation

The most updated documentation for scoary is found at the project site

Citation

If you use Scoary, please citing our paper

License

Scoary is freely available under a GPLv3 license.

Contact

Ola Brynildsrud (ola.brynildsrud@fhi.no)

Release History

Release History

This version
History Node

1.6.11

History Node

1.6.10

History Node

1.6.9

History Node

1.6.1

History Node

1.6.0

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
scoary-1.6.11-py2.py3-none-any.whl (284.4 kB) Copy SHA256 Checksum SHA256 2.7 Wheel Mar 31, 2017
scoary-1.6.11.tar.gz (257.6 kB) Copy SHA256 Checksum SHA256 Source Mar 31, 2017

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