The MABE to standard phylogeny converter can be found in ./mabe_converters/phylogeny.py
This converter can be used as either a command line tool (usage below) or be imported and used as a function in your own python scripts.
User must provide:
- mabe file format for files to convert: either snapshot or SSwD (snapshot with delay)
- other parameters are optional... see usage.
usage: phylogeny.py [-h] [-path PATH] [-fileType TYPE]
[-output_file_path OUTPUT_FILE_PATH] [-format FORMAT]
[-verbose] [-oldColumnNames COLUMN_NAME [COLUMN_NAME ...]]
[-newColumnNames COLUMN_NAME [COLUMN_NAME ...]]
Converts .csv files generated by MABE to the standard phylogeny format
optional arguments:
-h, --help show this help message and exit
-path PATH path to files - default : none (will read files in
current directory)
-fileType TYPE type of file, either snapshot or SSwD; default:
snapshot
-output_file_path OUTPUT_FILE_PATH, -out OUTPUT_FILE_PATH
Name to assign to standard-compliant output file.
-format FORMAT, -f FORMAT
What standard file format should this script output?
Valid options: ['csv', 'json']
-verbose adding -verbose will provide more text output while
running (useful if you are working with a lot of data
to make sure that you are not hanging) - default (if
not set) : OFF
-oldColumnNames COLUMN_NAME [COLUMN_NAME ...]
column names of data to read from source files -
default : "score_AVE" ("ID", "timeOfBirth", and the
correct ancestors list are added to the list
automatically)
-newColumnNames COLUMN_NAME [COLUMN_NAME ...]
column names of data to be copied into new data file -
default : NONE, if blank, copy oldColumnNames ("id",
"origin_time", and "parents" are added to the list
automatically)
- Cliff Bohm