MafTools

1 Overview | 2 Using | 2.1 Command Line Tools | 2.2 Using the Python Packages

Overview

This is a suite of the following three tools:

mafTools a collection of tools that operate on Multiple Alignment Format (maf) files.
Which depends on:
- sonLib is a compact C/Python library for sequence analysis in bioinformatics.
- pinchesAndCacti: This is a library for creating pinch graphs (generalised overlap graphs) and cactus graphs.

Using

Use the module name maftools to discover versions available and to load the application.

Command Line Tools

The various command line tools do not have any dependencies and use the current base system gcc compile:

[salexan5@tlog2 ~]$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

mafTools provides the following commands:

mafComparator  mafDuplicateFilter  mafFilter       mafPairCoverage    mafRowOrderer  mafStats     mafToFastaStitcher    mafValidator.py
mafCoverage    mafExtractor        mafPairCounter  mafPositionFinder  mafSorter      mafStrander  mafTransitiveClosure

and sonLib/pinchesAndCacti:

3EdgeTests  sonLib_cigarTest  sonLib_daemonize.py  sonLib_fastaCTest  sonLib_kvDatabaseTest  sonLibTests  stPinchesAndCactiTests

Simply type the command from the command line:

Using the Python Packages

mafTools depends on python 2.7 and the scipy numpy modules.

To use these you will need to load a python module and install scipy/numpy into your local folder. The example below first details the error you’ll see if these python modules are not installed into your local home folder, and then how to install them.

Import sonLib into Python: