Installation

mapmuts is written in Python. In addition to the pure Python code, it also has a few C-extensions which require a C compiler (such as gcc).

Dependencies

Although the core of mapmuts package can be run just using the standard Python libraries, there are lots of useful features that require the following external packages:

• mapmuts has been tested on Linux and Mac OS X.

• mapmuts requires Python. It has been tested with the following Python versions:

  • 2.6.8
  • 2.7.3

• The graphing performed by mapmuts requires matplotlib. It is known to work with the following matplotlib versions:

  • 1.2.1
  • 1.3.1

• Automatic compilation of plots into PDF summaries requires pdflatex.

• numpy is required for some operations. mapmuts has been tested with the following numpy versions:

  • 1.6.1
  • 1.7.1

• The MCMC Bayesian inference of the amino-acid preferences (or enrichment ratios) requires pymc. mapmuts has been tested with pymc version 2.3. It may not work with other versions of pymc.

• A few operations require scipy. The following versions of scipy have been tested:

  • 0.9.0
  • 0.12.0

• Creation of sequence logos requires installation of weblogo in a location that puts it in the current search path so that it can be run from the shell. This package has been tested with weblogo version 3.4. It is not known if it would work with other versions. Note that if weblogo crashes with a Ghostscript error, you may want to see this bug report. Some of the functionality also requires installation of the Python weblogo library (weblogolib) in a location that can be imported into Python.

• Overlay of RSA and SS information on the sequence logos requires the pyPdf package to be installed. This package has only been tested with pyPdf version 1.13 – it is unknown whether it would work with pyPdf2.

• The rpy2 package is required for the mapmuts_entropycomparison.py script. This package has been tested with version 2.3.9.

• The R statistical package is required for the mapmuts_entropycomparison.py script. This package has been tested with version 3.0.3.

Installation

To install mapmuts, first download the source ZIP repository on GitHub. After unzipping the file, run the following commands:

cd mapmuts
python setup.py build
python setup.py test
python setup.py install

The last command might need to be replaced with:

sudo python setup.py install

if you want to install the package globally do not have privileges to the default global installation directory. Alternatively, if you just want to install the package locally for the current user, you can use:

python setup.py install --user

The test command runs a variety of tests to check that the program appears to be working properly. This is optional, and the tests may take a few minutes to run. Running these tests is recommended.

These commands install the Python modules and also install several scripts, which provide the most convenient high-level interface into mapmuts package. There is also an ./examples/ subdirectory in the main mapmuts directory that contains some examples. Looking at these examples may be helpful for understanding the typical workflow.