Currently Unix/Linux and Mac OS-X are supported. A setup.py script is provided so installation is standard for python:
python setup.py build python setup.py install
To check that SpliceGrapher is installed correctly, run the python interpreter and type the following:
>>> import SpliceGrapher >>> SpliceGrapher.__version__ '0.2.5'
To test your installation more thoroughly, use the test script in the SpliceGrapher examples sub-directory:
cd examples run_tests.sh
SpliceGrapher uses highly accurate splice-site models to filter output from popular spliced alignment tools such as TopHat and MapSplice by removing potentially spurious novel junctions (see our publication in Genome Biology for details). We provide a simple script to do this:
sam_filter.py SAM-file classifiers -f FASTA-reference -m gene-models -o output-SAM
For example, reads aligned to the GRCh37 version of the H. sapiens genome with TopHat could be filtered as follows:
sam_filter.py accepted_hits.sam Homo_sapiens.zip -f Homo_sapiens.GRCh37.68.dna.toplevel.fa -m Homo_sapiens.GRCh37.68.gtf -o filtered.sam
SpliceGrapher’s primary objective is to predict splice graphs, which is accomplished using the program predict_graphs.py. It can combine evidence provided by gene models, EST alignments and NGS alignments to predict splice forms for a gene. The most common approach is to use NGS alignments:
predict_graphs.py SAM-file -d prediction-directory
For example, assuming reads have been filtered as outlined in the H. sapiens example above, one could make predictions for all human genes as follows:
predict_graphs.py filtered.sam -m Homo_sapiens.GRCh37.68.gtf -d predicted
Splice graphs are stored in the predicted directory, organized by chromosome. For example, the output graph for the gene SLC35B2 from chromosome 6 would appear in the file predicted/6/SLC35B2.gff. The splice graph output GFF format is used by all of SpliceGrapher’s plotting and viewing tools.
To view one or more splice graphs, use the view_splicegraphs.py script. For example, to view the graph stored in SLC35B2.gff, simply enter:
This produces a figure of the splice graph with minimal annotations, but the script also provides options for adding details to the figures. Also see the plotter.py tool that provides facilities for plotting publication-quality figures.