gtmanipulator Package

Contents:

• gtmanipulator source code
• Gt GUI source code (windowed and non-windowed versions)
• Sample data
• Unit tests

Installation:

Using pip: pip install gtmanipulator

Using setup.py:

1. Download the github repository: gtmanipulator
2. Extract the repository form the zip file
3. Navigate to the directory containing the setup.py file
4. pip install .

API

Use:

# Importing and summarizing
import gtmanipulator at gt
data = "some_data_file.csv"
manipulator = gt.GtManipulator(data)
summarizedDf = manipulator.summarize()
print(summarizedDf.head())

# Calculating allelic frequencies
freqDf = manipulator.calc_frequencies(missing={"??"})
print(freqDf)

# Setting definitions of morphisms and predicting morphisms
morphedDf = manipulator.predict_morphisms(failed=0.20, mono=0.80,
                                          poly={"Type 1": (0.80, 0.20, 0.10),
                                                "Type 2": (0.80, 0.10, 0.20),
                                                "Type 3": (0.10, 0.10, 0.10)},
                                          comp_ops={"Type 1": ("<", ">", "<="),
                                                    "Type 2": ("<", "<=", ">"),
                                                    "Type 3": (">", ">", ">")})
print(morphedDf)

# Saving
manipulator.save("some_file.csv")

# Transposing
manipulator.transpose()

GUI

Use:

In order to run the Gt Gui you must first have properly installed the gtmanipulator package. You may then run the GUI with or without a console. To run without a console simply double-click on the gtgui.pyw file. To get the GUI files download the gtmanipulator repository and extract the zip file. Then navigate to the gtgui directory where the gtgui.py and gtgui.pyw files can be found.

Notes

Additional documentation and instructions can be found in the docstrings of the API or in the tooltips within the GUI.

For any other questions email: travis.m.couture@gmail.com