GA-TA program is used to convert an easy-to-build generic table into more complex tables in the specific format required to use with Structure, Arlequin, and R softwares. GA-TA is applicable to autosomic, mitochondrial and X chromosome data. The program is written in Python under an open source policy, allowing experienced users to download the program from the github repository (https://github.com/santimda/GA-TA) and adapt it by adding new modules upon convenience.
A stable version of the program can be executed on a friendly user environment on this GA-TA website.
GA-TA is a Python module. You can install in your local environment doing:
$ python setup.py install
and you can enjoy GA-TA as Python3 module. You have a pipeline called main.py as an example of how to wrok with it.
To execute the example from the command line, run:
$ python main.py [OPTIONS] <spreadsheet_name>
.. Install miniconda .. Create myenv $ conda create -n myenv python=3.X .. Activate environment $ conda activate myenv .. Install the following packages using 'conda install pack': . pandas . xlrd . unidecode . openpyxl
[OPTIONS]: The user can specify one, two or three letters (in any order) to obtain the desired output tables. These are: "r" for R, "a" for Arlequin, and "s" for Structure.
The spradsheet must be either in Excel extention '.xlsx' or in open office '.ods'
Examples:
>$ python main.py ra spreadsheet.xlsx
will return output files for R and Arlequin.
>$ python main.py s spreadsheet.xlsx
will return output files for Structure.
All columns with information must have a name (e.g., there cannot be a blank cell in the first row for any column with information). An example sheet along with a more detailed manual can be downloaded from the GA-TA website, and they are also available in the folder 'Documentation'.