| Name | gopiscator JSON |
| Version |
0.1.5
JSON |
| download |
| home_page | None |
| Summary | CLI tool for performing gene set enrichment analysis using the GO database. |
| upload_time | 2024-08-26 22:42:45 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT License Copyright (c) 2024 Dmitry Bespiatykh Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
go
enrichment
gene
ontology
fisher
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<p align="center">
<img src="https://github.com/dbespiatykh/gopiscator/blob/main/logo.png?raw=true" alt="gopiscator logo" height=200>
</p>
<hr>
`GOpiscator` is a command-line tool for performing gene set enrichment analysis using the Gene Ontology (GO) database.
[](https://badge.fury.io/py/gopiscator)
### 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.
```
<hr>
> [!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 |
<hr>
> [!TIP]
> <details>
> <summary>If you do not provide <code>-o, --output</code> then the results will be shown in terminal like this:</summary>
>
>```
>╒════╤════════════╤════════════════════╤═══════════════════════════════╤═══════════╤════════════════════╤═══════════════╕
>│ │ 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 │
>╘════╧════════════╧════════════════════╧═══════════════════════════════╧═══════════╧════════════════════╧═══════════════╛
>```
>
></details>
>
> <details>
> <summary>When the <code>-o, --output</code> is provided the the output file will look like this:</summary>
>
>| 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 |
>
> </details>
Raw data
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"description": "<p align=\"center\">\n <img src=\"https://github.com/dbespiatykh/gopiscator/blob/main/logo.png?raw=true\" alt=\"gopiscator logo\" height=200>\n</p>\n<hr>\n\n`GOpiscator` is a command-line tool for performing gene set enrichment analysis using the Gene Ontology (GO) database.\n\n[](https://badge.fury.io/py/gopiscator)\n\n### Installation\n\n```\npip install gopiscator\n```\n\n### Usage\n\n```\nUsage: gopiscator [OPTIONS]\n\n GOpiscator (Tool for performing gene set enrichment analysis)\n\nOptions:\n -i, --gene-list FILE Genes of interest list. [required]\n -a, --go-annotation FILE GO annotation file. [required]\n -o, --output FILE Write output to a file. [default: (standard output)]\n -g, --ontology FILE GO '.obo' file. [default: ('go-basic.obo'; will be downloaded if absent)]\n -b, --background-list FILE Background gene list file. [default: (All genes from 'go-annotation' file)]\n --threshold FLOAT P-value threshold. [default: 0.05]\n --gene-count INTEGER Minimum No. of genes annotated to the specific GO term. [default: 2]\n -v, --version Show the version and exit.\n -h, --help Show this message and exit.\n```\n<hr>\n\n> [!NOTE]\n> `gene-list` should have your genes of interest, one gene per line:\n> ||\n>| --- |\n>| Rv3861 |\n>| Rv3862c |\n>| Rv0083 |\n>| Rv3371 |\n>\n> `go-annotation` should be tab-delimited with genes in the first column and GO terms in the second column (separated by comma):\n> |||\n>| --- | --- |\n>| Rv0001 |\tGO:0006172,GO:0006275,GO:0006270 |\n>| Rv0002 |\tGO:0046677,GO:0006260 |\n>| Rv0003 |\tGO:0009432,GO:0000731,GO:0006260 |\n>| Rv0005 |\tGO:0046677,GO:0006265,GO:0006261 |\n>\n> `background-list` if you want to use background list of genes, it should have one gene per line:\n> ||\n>| --- |\n>| Rv0001 |\n>| Rv0002 |\n>| Rv0003 |\n>| Rv0005 |\n\n<hr>\n\n> [!TIP]\n> <details>\n> <summary>If you do not provide <code>-o, --output</code> then the results will be shown in terminal like this:</summary>\n>\n>```\n>\u2552\u2550\u2550\u2550\u2550\u2564\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2564\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2564\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2564\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2564\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2564\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2555\n>\u2502 \u2502 GOID \u2502 Ontology \u2502 GO_term_name \u2502 P-value \u2502 Enrichment_score \u2502 Rich_factor \u2502\n>\u255e\u2550\u2550\u2550\u2550\u256a\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u256a\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u256a\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u256a\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u256a\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u256a\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2550\u2561\n>\u2502 0 \u2502 GO:0045926 \u2502 biological_process \u2502 negative regulation of growth \u2502 0 \u2502 4.36 \u2502 0.2 \u2502\n>\u251c\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2524\n>\u2502 1 \u2502 GO:0098754 \u2502 biological_process \u2502 detoxification \u2502 0.015 \u2502 1.82 \u2502 0.2 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