MPAthic

Quantitative Modeling of Sequence-function Relationships for Massively Parallel Assays

*Written by Ammar Tareen*

Under Active Development

MPAthic [1] is a python API and it infers quantitative models from data. Most MPAthic classes take in one or more tabular text files as input and return a tabular text file as output. All input and output files are designed to be human readable. The first line of each tabular text file contains headers describing the contents of each column. All input files are required to have the proper set of columns, which of course depend on the command being executed. By default, input is taken from the standard input and output is written to the standard output.

_images/S0.png _images/S1.png

Installation

Prerequisites

MPAthic uses some Non-python resources and has the following prerequisites for installation:

  • GCC

    GCC, which contains both C compilers and Fortran compilers, is required to run MPAthic. From with in terminal, run the command gcc.

    $ gcc
$ clang: error: no input files

    Check that gfortran was installed with gcc.

    $ gfortran
$ gfortran: fatal error: no input files ...
  • NUMPY

    numpy is required to be installed before mpathic can be installed.

    pip install numpy

Install MPAthic

With the prerequisites installed, MPAthic can be installed using the pip (version 9.0.0 or higher) from PyPI. At the command line:

pip install mpathic

The code for MPAthic is open source and available on GitHub. Some commonly encountered installation issues can be found here: Common Installation Issues

Quick Start

The following snippets show how to use MPAthic from within python.

import mpathic as mpa
mpa.demo()

Contact

For technical assistance or to report bugs, please contact Ammar Tareen.

For more general correspondence, please contact Justin Kinney.

Other links:

Indices and tables