SpliceGrapher Files

SpliceGrapher - predicting splice graphs from diverse evidence
Mark F. Rogers
rogersma@cs.colostate.edu
Version 0.2.7 released 


Description
===========
SpliceGrapher is a Python-based scripting tool that uses gene models, RNA-Seq data
and ESTs to predict splice graphs that capture in a single structure all the ways
in which a gene's exons may be assembled.  In a splice graph, a gene's exons are
depicted as vertices and introns are depicted as edges between them.  The compact
structure allows researchers to visualize a gene's AS patterns more easily than by
examining separate transcripts.

SpliceGrapher includes modules that may be incorporated anywhere in an RNA-Seq
analysis pipeline from initial alignment to final splice graph prediction.  The
package includes modules for constructing a database of known, recombined and
predicted splice-junction sequences that may be used with ungapped short-read
alignment algorithms such as MAQ, BowTie or PASS.  The prediction modules are
able to incorporate gene models in GFF3 format, RNA-Seq alignments in SAM format
or EST alignments in PSL format.  The viewing modules are able to read these
same files to produce plots that depict a predicted graph along with the evidence
SpliceGrapher used to produce it.

Currently SpliceGrapher supports RNA-Seq alignments in SAM, BED and WIG formats,
EST alignments in PSL format and Cufflinks transcript descriptions in GTF format.


Installation
============
Only Unix/Linux/OS-X is supported.

Requirements:
   matplotlib http://matplotlib.sourceforge.net     (version 2.1.0 or higher)
   PyML       http://sourceforge.net/projects/PyML  (version 0.7.14 or higher)

A setup.py script is provided so installation follows the standard python idiom:

>>> python setup.py build
>>> python setup.py install

To install in a different directory than the system default, use

>>> python setup.py install --home=/my/python/packages

You may also install the stand-alone scripts in their own separate directory using
the format:

>>> python setup.py install --home=/my/python/packages --install-scripts=/my/python/scripts


Updating paths
==================
Before you run SpliceGrapher scripts, you will want to add the correct path to your
PATH environment variable.  By default this will be the /bin directory directly under
the main installation directory.  If you chose a different script path using the
--install-scripts option, then use that path instead.

If you used '--home=' to specify a home directory other than the default, you must
ensure that it is included in your PYTHONPATH directory before you try to access
SpliceGrapher's modules from python.


Running Examples
================
The 'examples' subdirectory of the distribution contains example data and a shell script
for creating splice graphs for the example data.  To test your installation, simply
run the script:

>>> cd examples
>>> run_tests.sh

This script also provides examples to get you started using the SpliceGrapher Python
scripts with your own data.


Documentation
=============
User Guide - doc/userguide.pdf
Examples - SpliceGrapher/examples