Genescape

Note: the suite is under development and not yet mature. The docs below may not always be accurate.

The genescape suite is a collection of tools used to visualize the results of functional genome analysis. Various new tools may be implemented in the future.

• tree draws informative Gene Ontology (GO) subgraphs
• annotate annotates a list of genes with GO functions

Demonstration data

We packaged demo data with the software so you can test the programs like so:

genescape tree --demo
genescape annotate --demo
genescape annotate --demo | genescape tree

See Installation on how to get started.

genescape tree

Starting with a file that contains GO terms (see goids.txt for the complete file) :

GO:0005488
GO:0005515
GO:0048029
GO:0005537
GO:0003824
...

run the tree command to visualize the relationships between the GO terms:

genescape tree goids.txt 

The command generates the following a file called output.pdf that contains:

Get more help with:

genescape tree -h

Read more about how genescape tree works.

genescape annotate

The annotator operates on gene names. Suppose you have a list of gene names in the format:

Cyp1a1
Sphk2
Sptlc2
Smpd3

The command:

genescape annotate names.txt 

will generate the file containing the top 10 most common functions across these genes:

goid,count,size,label,function
GO:0005515,3,5,3/5,protein binding
GO:0046512,2,5,2/5,sphingosine biosynthetic process
GO:0043231,2,5,2/5,intracellular membrane-bounded organelle
GO:0030148,2,5,2/5,sphingolipid biosynthetic process
GO:0005789,2,5,2/5,endoplasmic reticulum membrane
GO:0005743,2,5,2/5,mitochondrial inner membrane
GO:0005737,2,5,2/5,cytoplasm
GO:2001169,1,5,1/5,regulation of ATP biosynthetic process
GO:2000304,1,5,1/5,positive regulation of ceramide biosynthetic process
GO:1904959,1,5,1/5,regulation of cytochrome-c oxidase activity
# INFO	gs_annotate.run	there are 147 additional terms not shown

The numbers in this file represent how many of your input genes were annotated with the given function relative to the total number of genes (4).

By default, it only shows the top 10 most common functions. You can change the cutoff with the -n 100 flag. Currently -n 0 would mean no limit.

Get more help with:

genescape annotate -h

Pipelining

Piping the output of genescape annotate into genescape tree will generate an image that visualizes the functional roles of the genes in the input file.

Here we filter for the functions that match regulation:

genescape annotate names.txt -n 0 -m regulation | genescape tree

The output is a functional map of the genes::

By default, only the top 10 most common functions are generated. That cutoff can be changed via the -t flag.

You also have the option to filter for certain functions

The human annotation file (GAF) is included in the distribution and will be used by default.

For other organisms, or to use the most up-to-date GAF for human, you would need to download the GAF file for your organism of interest and provide it to the annotator like so -g goa_human.gaf.gz. The GAF files are available on the GO website.

Installation

To generate images from the command line, you will need to have the dot software from Graphviz installed and available on your PATH. You can install Graphviz via your package manager or via conda with:

conda install graphviz

The software requires Python 3.9 or above. You can install genescape via pip or pipx.

Since the software is meant to be used as a command line tool, pipx is the recommended approach.

pipx install genescape

Alternatively, you can also use pip to install:

pip install genescape

If you are unable to install the dot package you can save the output as .dot files

genescape tree -o graph.dot --demo

Then use an online tool like viz-js to visualize the graph.

License

genescape is distributed under the terms of the MIT license.