roary2fripan

Formats Roary output for viewing in FriPan

Author

Jason Kwong (@kwongjc)
GitHub: kwongj

Dependencies

• Python 3.x

Usage

$ roary2fripan.py -h

usage: 
  roary2fripan.py [OPTIONS] <PREFIX>

Script to format Roary output for FriPan

positional arguments:
  PREFIX        Specify output prefix

optional arguments:
  -h, --help    show this help message and exit
  --input FILE  Specify Roary output (default = "gene_presence_absence.csv")
  --version     show program's version number and exit

Basic syntax

Requires output file "gene_presence_absence.csv" from Roary

$ roary2fripan.py --input gene_presence_absence.csv <prefix>

This produces three files:

• <prefix>.proteinortho (array of gene presence/absence)
• <prefix>.descriptions (annotations for genes)
• <prefix>.strains (list of strains - can be re-ordered and categories added for displaying in FriPan)

These three files can be loaded into FriPan for viewing. See links below.

Bugs

Please submit via the GitHub issues page: https://github.com/kwongj/roary2fripan/issues

Software Licence

GPLv2: https://github.com/kwongj/roary2fripan/blob/master/LICENSE

Links

• Roary by Andrew Page - https://github.com/sanger-pathogens/Roary
• FriPan by David Powell - http://drpowell.github.io/FriPan/