https://github.com/giuliacassara/variationfinder
A re-implementation in Python3 of the open source project MutationFinder for gene mutation detection in free text.
https://github.com/giuliacassara/variationfinder
bioinformatics genetics mutations
Last synced: 11 months ago
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A re-implementation in Python3 of the open source project MutationFinder for gene mutation detection in free text.
- Host: GitHub
- URL: https://github.com/giuliacassara/variationfinder
- Owner: giuliacassara
- Created: 2020-09-20T19:03:47.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2020-09-20T19:22:22.000Z (almost 6 years ago)
- Last Synced: 2025-03-01T18:30:08.532Z (over 1 year ago)
- Topics: bioinformatics, genetics, mutations
- Language: Python
- Homepage:
- Size: 403 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# VariationFinder
A re-implementation in Python3 of the open source project MutationFinder for gene mutation detection in free text http://mutationfinder.sourceforge.net/
## Features
* Recognizes WNM, RSID and c.Na>a genomic variant notations, including natural language forms
* More genomic variant notations will be added later, based on this table https://academic.oup.com/view-large/206216442
## Usage
from the terminal type:
```
./mutation_finder.py corpora/test_set.txt
```
Output file is test_set.txt.mf in the same directory of mutation_finder.py
## References
```
MutationFinder: A high-performance system for extracting point mutation mentions from text
J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter; Bioinformatics, 2007 23(14):1862-1865; doi:10.1093/bioinformatics/btm235;
```