Light wrapper for the R topGO package that produces interactive GO enrichment html reports
Project description
GOldwasher is a light wrapper for the R package topGO (https://bioconductor.org/packages/release/bioc/html/topGO.html). The function of GOldwasher is limited to the calculation of GO term enrichment (via elimFisher algorithm) of target gene lists and also the generation their respective GO subgraph images (via Graphviz (http://www.graphviz.org/) - Graph Visualization Software) subsuming their annotations. These elements are then incorporated together into html a single report file per input list which can then be interactively explored. The purpose and focus of this module is to facilitate batch processing of several gene lists.
Current release: 0.2.1 (alpha)
Provides basic functionality and basic documentation. Methods and functions are working if the input does not deviate from expected (none to little input sanitization) but they haven’t been extensively tested.
TODO:
Write (proper) tests
Improve documentation
Re-think R interface mod
Make OBOe mod independent of ontology mod
Extend functionality (select and compare subsets)
Installation
# pip install GOldwasher-0.2.1.tar.gzor
# pip install GOldwasherRequirements: The non-python dependencies are:
graphviz http://www.graphviz.org/
topGO http://bioconductor.org/packages/release/bioc/html/topGO.html (and inherently R)
GO OBO file (http://geneontology.org/page/download-ontology)
These packages/file should be installed/downloaded for GOldwasher to work. All other python dependencies should be automatically resolved by pip.
Usage
GOldwasher can be used as a module, making use of its methods, or more easily it can conveniently be used from its command tool ‘goldpanner’
goldpanner [-h] -c CONFIG -i INPUTDIR
{SPLIT,ANNOT,ENRICH,DAG,REPORT}e.g.:
goldpanner -c settings.ini -i lists/ REPORT-c ini file with general settings using the following structure:
[vars]
alpha = 0.01
organism = phaeodactylum
[sources]
functionalDesc = /path/to/tabseparedfile/withIDtabFunctionalDescription.txt
g_map = /path/to/mappings/identifier2GOaccessions.txt
obofile = /path/to/go-basic.obo
#linkinsets = /path/to/custom/organisms.json
[vars]
alpha - significance level
organism - name of the organism (as key name on ‘organisms.json’)
[sources]
functionalDesc
path to tab-separated file holding a column of identifiers and their matching functional descriptors.
g_map
path to tab-separated file holding a column of identifiers and a second column with their associated GO term accession numbers separated by commas.
e.g.:
Phatr3_J43587.t1 GO:0006396,GO:0005622,GO:0005515
obofile
path to the GO ontology obo file. It can be downloaded from: http://purl.obolibrary.org/obo/go/go-basic.obo
linkinsets
If using organisms other than Arabidopis thaliana or Phaeodactylum tricornutum uncomment this variable and set it as the path to the customized ‘organisms.json’. By default no cross-links are generated for unknown/unset organisms.
-i directory with the target lists.
COMMANDS:
SPLIT - splits baySeq result files (pairwise conditions) into up and down-regulated lists.
ANNOT - annotates identifiers lists with respective available functional descriptors.
ENRICH - performs GO term enrichment on the annotated lists.
DAG - generates color-coded GO graph image (svg format) from (topGO) enrichment results.
REPORT - generates an interactive html GO enrichment report for each list on the input directory.
optional argument:
-o output directory (can be used with all commands except ENRICH)
Acknowledgements
3rd party libraries — Additional required 3rd party content is also bundled together with the source code for this program. That content is listed below along with the licenses under which they have been released.
