SpliceGrapher - predicting splice graphs from diverse evidence
Mark F. Rogers
Version 0.2.4 released
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.
Only Unix/Linux/OS-X is supported.
matplotlib http://matplotlib.sourceforge.net (version 1.0.0 or higher)
PyML http://sourceforge.net/projects/PyML (version 0.7.7 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
>>> python setup.py install --home=/my/python/packages --install-scripts=/my/python/scripts
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.
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
This script also provides examples to get you started using the SpliceGrapher Python
scripts with your own data.
User Guide - doc/userguide.pdf
Examples - SpliceGrapher/examples