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FofanovLab / VaST

Variant Site Strain Typer: Identifies the minimum number of variable genomic site that are required to resolve a group of related bacterial strains
MIT License
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Pattern Selection Module Output files #4

Open shashidr opened 5 years ago

shashidr commented 5 years ago

Hi Tara,

Could you please add more documentation on the pattern selection module output files? My pattern selection module analysis completed and now want to figure out the output file formats.

Thanks,

Shashi

tfursten commented 5 years ago

@shashidr Hi Shashi, you can run VaST/analyze.py to get some better summary files of the pattern selection output. 

python VaST/analyze.py --help
usage: VaST Analyze Results [-h] [--sep {tab,comma,space}] [--log LOG]
                            PROJECT_DIR VAR_MATRIX_PATH

Analyze and format pattern selection ouput

positional arguments:
  PROJECT_DIR           Path to pattern selection directory
  VAR_MATRIX_PATH       Path to variant site matrices.

optional arguments:
  -h, --help            show this help message and exit
  --sep {tab,comma,space}
                        Specify the file delimiter of variant site matrix
                        (default: tab)
  --log LOG             Path to log file. (default: ./VaST_analysis.log)

The most recent update to the pattern selection module will output these files automatically if you want to rerun the pattern_selection module on your data. I have added some documentation to the readme to describe the output.