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.

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.