GOldwasher 0.2.8

Light wrapper for the R topGO package that produces interactive GO enrichment html reports

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.

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Current release: 0.2.8 (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.

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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-0.2.8.tar.gz

or

# pip install GOldwasher

Requirements: The non-python dependencies are:

• graphviz http://www.graphviz.org/

• GO OBO file (http://geneontology.org/page/download-ontology)

R packages (and inherently R):

• topGO http://bioconductor.org/packages/release/bioc/html/topGO.html

• jsonlite https://cran.r-project.org/web/packages/jsonlite/index.html

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
              {ANNOT,ENRICH,DAG,REPORT}

e.g.:

goldpanner -c settings.ini -i lists/ REPORT

-c ini file with general settings using the following structure:

[meta] [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:

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.

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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.

> OBO Ontology python module

http://pythonhosted.org/Orange-Bioinformatics/

Copyright (c) Bioinformatics Laboratory, FRI UL

Released under the GNU General Public License license

> Sortable tables

http://www.kryogenix.org/code/browser/sorttable/

Copyright (c) Stuart Langridge

Released under the X11 (MIT) license

http://www.kryogenix.org/code/browser/licence.html

> jQuery

Copyright (c) jQuery Foundation and other contributors

Released under the MIT license:

http://jquery.org/license

> SVGPan v3.2.9

https://github.com/ariutta/svg-pan-zoom

Copyright (c) Andrea Leofreddi

The code from the SVGPan library is licensed under the following BSD license

https://raw.githubusercontent.com/ariutta/svg-pan-zoom/master/LICENSE

> Tabbed Content v2013.7.6

http://www.menucool.com/tabbed-content

Free to use