raymondkiu / cfml-maskrc

Masks recombinant regions in an alignment based on ClonalFrameML output

cfml-maskrc

Masks recombinant regions in an alignment based on ClonalFrameML output
Option to draw SVG of recombinant regions

Author

Jason Kwong (@kwongjc)
GitHub: kwongj

Dependencies

• Python 3.x
• BioPython
• ete3
• svgwrite

Usage

$ cfml-maskrc.py -h

usage: 
  cfml-maskrc.py --aln FASTA --out OUTFILE <CFML_PREFIX>

Script to mask recombination from ClonalFrameML output and draw SVG of recombinant regions

positional arguments:
  CFML_PREFIX          prefix used for CFML output files (required)

optional arguments:
  -h, --help           show this help message and exit
  --aln FASTA          multiFASTA alignment used as input for CFML (required)
  --out OUTFILE        output file for masked alignment (default="maskrc.aln")
  --symbol ?           symbol to use for masking (default="?")
  --regions FILE       output recombinant regions to file
  --svg FILE           draw SVG output of recombinant regions and save as specified file
  --svgsize WIDExHIGH  specify width and height of SVG in pixels (default="800x600")
  --svgorder FILE      specify file containing list of taxa (1 per line) in desired order
  --svgcolour COLOUR   specify colour of recombination regions in HEX format (default=black)
  --consensus          add consensus row of recombination hotspots
  --version            show program's version number and exit

Requires:

• Output from ClonalFrameML (specify prefix used to name output files)
• MultiFASTA alignment used as input for ClonalFrameML

Options:

• Specify output file using --out OUTFILE
• Specify symbol to use in the alignment for masking --symbol ?
• Save tab-separated file of recombinant region coordinates --regions FILE
• Draw SVG of recombinant regions --svg FILE
• Specify size of SVG in pixels eg. 800x600 --svgsize WIDTHxHEIGHT
• Specify desired order of taxa in SVG --svgorder FILE
• Specify colour to show extant recombination --svgcolour COLOUR
• Add consensus row of recombination hotspots to SVG --consensus

Bugs

Please submit via the GitHub issues page: https://github.com/kwongj/cfml-maskrc/issues

Software Licence

GPLv2: https://github.com/kwongj/cfml-maskrc/blob/master/LICENSE

Other links

• ClonalFrameML