CLI tool for performing gene set enrichment analysis using the GO database.
Project description
GOpiscator
is a command-line tool for performing gene set enrichment analysis using the Gene Ontology (GO) database.
Installation
pip install gopiscator
Usage
Usage: gopiscator [OPTIONS]
GOpiscator (Tool for performing gene set enrichment analysis)
Options:
-i, --gene-list FILE Genes of interest list. [required]
-a, --go-annotation FILE GO annotation file. [required]
-o, --output FILE Write output to a file. [default: (standard output)]
-g, --ontology FILE GO '.obo' file. [default: ('go-basic.obo'; will be downloaded if absent)]
--threshold FLOAT P-value threshold. [default: 0.05]
--gene-count INTEGER Minimum No. of genes annotated to the specific GO term. [default: 2]
-v, --version Show the version and exit.
-h, --help Show this message and exit.
[!NOTE]
gene-list
should have your genes of interest, one gene per line:
Rv3861 Rv3862c Rv0083 Rv3371
go-annotation
should be tab-delimited with genes in the first column and GO terms in the second column (separated by comma):
Rv0001 GO:0006172,GO:0006275,GO:0006270 Rv0002 GO:0046677,GO:0006260 Rv0003 GO:0009432,GO:0000731,GO:0006260 Rv0005 GO:0046677,GO:0006265,GO:0006261
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