gopiscator 0.1.0

CLI tool for performing gene set enrichment analysis using the GO database.

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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