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Installation and usage (MOODS 1.0)
This is the installation and usage documentation for the old MOODS 1.0. For the latest version of MOODS, refer to MOODS Github page.
Download MOODS_1.0.2.tar.gz from the MOODS main page (http://www.cs.helsinki.fi/group/pssmfind/) and extract it:
tar -xvzf MOODS_1.0.2.tar.gz
Under the MOODS directory, the C++ algorithm implementation library is under src/ directory, Perl and Python interfaces under their respective directories, and examples/ directory contains example scripts.
You need to compile the C++ library before installing the Perl and Python interfaces:
cd src/
make
You can link your own C++ programs with this library; all the necessary declarations are in the header file pssm_algorithms.hpp. There is also a command line tool for basic tasks (see src/find_pssm_dna_readme.txt).
The setup.py script is used to install the MOODS python interface. It requires Python.h C headers, so you may have to install Python development packages before compiling the interface.
The python interface requires that you have compiled the C++ library as instructed above.
cd python
python setup.py install
Examples of Python interface usage. These are also included in MOODS package.
- Example 1 — Basic usage
- Example 2 — Searching multiple matrices at the same time
- Example 3(a) — Full MOODS workflow using the default scoring model
- Example 3(b) — Full MOODS workflow using a custom scoring model
- MOODS This module contains an interface to PWM search algorithms.
MOODS Perl interfaces depend on BioPerl, so you need to have it installed. On many Linux distributions, it is directly available from the package management system.
To compile the Perl interfaces, first make sure that you have compiled the C++ library as instructed above.Then proceed as follows.
cd perl
perl Makefile.PL
make
If you want to use non-standard installation path, use command
perl Makefile.PL PREFIX=/path/
For more details see perl documentation here.
Installing may need administrator privileges:
make install
Following examples demonstrate the basic usage of MOODS Perl interfaces. You can find the same examples also from MOODS package.
- Example 1 — Basic usage
- Example 2 — Searching multiple matrices at the same time
- Example 3 — Loading matrix files and tuning the scoring model parameters
- Window search — A more complicated example on processing the results; finds from a given DNA sequence a window of given width such that this window has large enough number of good enough binding sites for a given set of matrices.
- MOODS The main search function.
- MOODS::Tools Tools for handling search data.