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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)]
  -b, --background-list FILE  Background gene list file.  [default: (All genes from 'go-annotation' file)]
  --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.

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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

background-list if you want to use background list of genes, it should have one gene per line:

Rv0001
Rv0002
Rv0003
Rv0005

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Tip

If you do not provide -o, --output then the results will be shown in terminal like this:

╒════╤════════════╤════════════════════╤═══════════════════════════════╤═══════════╤════════════════════╤═══════════════╕
│    │ GOID       │ Ontology           │ GO_term_name                  │   P-value │   Enrichment_score │   Rich_factor │
╞════╪════════════╪════════════════════╪═══════════════════════════════╪═══════════╪════════════════════╪═══════════════╡
│  0 │ GO:0045926 │ biological_process │ negative regulation of growth │     0     │               4.36 │           0.2 │
├────┼────────────┼────────────────────┼───────────────────────────────┼───────────┼────────────────────┼───────────────┤
│  1 │ GO:0098754 │ biological_process │ detoxification                │     0.015 │               1.82 │           0.2 │
╘════╧════════════╧════════════════════╧═══════════════════════════════╧═══════════╧════════════════════╧═══════════════╛

When the -o, --output is provided the the output file will look like this:

GOID	Ontology	GO_term_name	Definition	P-value	FDR	Enrichment_score	Fold_enrichment	Rich_factor	GeneRatio	BgRatio	Count	Genes
GO:0045926	biological_process	negative regulation of growth	Any process that…	4.40E-05	0.00171655	4.35640751	9.81395349	0.1627907	7[35]	43[2110]	7	Rv0299,Rv0609,Rv1114,Rv2010,Rv2866,Rv3384c,Rv3697c
GO:0098754	biological_process	detoxification	Any process that…	0.01503798	0.29324058	1.82281055	15.0714286	0.25	3[35]	12[2110]	3	Rv1560,Rv2550c,Rv2801A