molyso2vizardous

You can convert molyso’s tabular output format to PhyloXML/MetaXML lineage trees for viewing and analysis with Vizardous see:

Helfrich, S. et al., 2015. “Vizardous: Interactive Analysis of Microbial Populations with Single Cell Resolution” Bioinformatics (Oxford, England). DOI: 10.1093/bioinformatics/btv468

You can download Vizardous at https://github.com/modsim/vizardous .

The appropriate tool is embedded in molyso in the molyso.util.molyso2vizardous package.

> python3 -m molyso.util.molyso2vizardous

usage: __main__.py [-h] [-o OUTPUT] [-d MINIMUM_DEPTH] [-q] input

molyso2vizardous molyso-tabular data format to Vizardous metaXML/phyloXML
converter

positional arguments:
  input                 input file

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
  -d MINIMUM_DEPTH, --minimum-depth MINIMUM_DEPTH
  -q, --quiet

error: the following arguments are required: input

> python3 -m molyso.util.molyso2vizardous results.txt

The tool will then generate many individual files for each found track (you can filter out too short tracks by using the -d MINIMUM_DEPTH option). Note that the internal XML representation is very memory consuming.