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
[!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 stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. [GOC:go_curators] 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 reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. [GOC:dos] 0.01503798 0.29324058 1.82281055 15.0714286 0.25 3[35] 12[2110] 3 Rv1560,Rv2550c,Rv2801A
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