GTFP: Initial public offering

This is a tagged release of the first publicly available release of these Python bindings that enable us to provide an interface to GTFold -- gtdmmb fork -- from within Python3. Please consult our WIKI documentation for instructions on how to build from source and for other pointers.

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If you run into problems installing or using this software, please feel free to submit a new issue for the developers on GitHub. Enjoy! 😺

gtDMMB tap brew installer for recent MacOS -- !!! TODO: NOT YET WORKING !!!

$ brew tap gtDMMB/homebrew-core
$ brew update
$ brew install --build-from-source --verbose gtDMMB/core/GTFoldPython3

Installation from source cribnotes (Linux)

If the next steps fail, please consult the full details of the install instructions on the WIKI. If you are confident, or bold, or feeling lucky, then run the following to install on Linux. Note that this procedure skips over the details about installing prerequisite packages and libraries:

$ git clone https://github.gatech.edu/gtDMMB/GTFoldPython.git
$ cd GTFoldPython/Python
$ make clean && make
... PATIENCE: THIS WILL TAKE A WHILE TO BUILD ...
$ make bash-configure
$ make test
... NOTE: THE PREVIOUS COMMAND IS STRICTLY OPTIONAL ...
... PATIENCE: THIS WILL TAKE A WHILE TO COMPLETE ...

Example of usage

Assuming you have successfully installed the software and have it configured correctly in your bash shell configuration (e.g., by running make bash-configure), the following provides an example of how to use this GTFold Python interface in a script:

import sys, os
from GTFoldPythonImportAll import *

GTFP.Init()
GTFP.Config(quiet = False, debugging = False, verbose = False, stdmsgout = "stderr")

baseSeqFPCons = "GCAUUGGAGAUGGCAUUCCUCCAUUAACAAACCGCUGCGCCCGUAGCAGCUGAUGAUGCCUACAGA"
consListFP = GTFPUtils.ReadFPConstraintsFromFile("../Testing/TestData/tRNA/yeast.fa.cons")

(mfe, mfeDOTStruct) = GTFP.GetMFEStructure(baseSeqFPCons, consListFP)
print("MFE %1.3f => MFE DOT STRUCT\n \"%s\"\n\n" % (mfe, mfeDOTStruct))

You can also refer to a more detailed example with comments here -- WIKI version -- or here -- direct script source --.