orthofisher
a broadly applicable tool for automated gene identification and retrieval
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
a broadly applicable tool for automated gene identification and retrieval
Basic Info
- Host: GitHub
- Owner: JLSteenwyk
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://jlsteenwyk.com/orthofisher/
- Size: 81.9 MB
Statistics
- Stars: 32
- Watchers: 2
- Forks: 1
- Open Issues: 3
- Releases: 4
Topics
Metadata Files
README.md
Docs · Report Bug · Request Feature
Orthofisher conducts automated and high-throughout identification of a predetermined set of orthologs, which can be used for phylgenomics, gene family copy number determination and more!
If you found orthofisher useful, please cite orthofisher: a broadly applicable tool for automated gene identification and retrieval. Steenwyk & Rokas 2021, G3 Genes|Genomes|Genetics. doi: 10.1093/g3journal/jkab250.
Guide
Quick Start
Performance Assessment
FAQ
Quick Start
For detailed instructions on usage and a tutorial, please see the online documentation.
1) Prerequisite
Before installing orthofisher, please first install HMMER3 and add the HMMER to your .bashrc path. For example, my .bashrc has the following:
shell
export PATH=$PATH:/home/steenwj/SOFTWARE/hmmer-3.1b2-linux-intel-x86_64/binaries
2) Install orthofisher
If you are having trouble installing orthofisher, please contact the lead developer, Jacob L. Steenwyk, via email or twitter to get help.
To install via anaconda, execute the follwoing command:
shell
conda install -c jlsteenwyk orthofisher
Visit here for more information: https://anaconda.org/jlsteenwyk/orthofisher
To install via pip, execute the follwoing command:
shell
pip install orthofisher
To install from source, execute the follwoing command: ```shell
download
git clone https://github.com/JLSteenwyk/orthofisher.git
change dir
cd orthofisher/
install
make install ```
If you run into software dependency issues, install orthofisher in a virtual environment. To do so, create your virtual environment with the following command: ```shell
create virtual environment
python -m venv .venv
activate virtual environment
source .venv/bin/activate ```
Next, install the software using your preferred method above. Thereafter, you will be able to use orthofisher.
To deactivate your virtual environment, use the following command: ```shell
deactivate virtual environment
deactivate ``` Note, the virtual environment must be activated to use orthofisher.
Performance Assessment
Using 1,530 sequence similarity searches across six model eukaryotic proteomes, the performance of orthofisher was compared to results obtained from BUSCO. Examination of precision and recall revealed near perfect performance. More specifically, orthofisher had a recall of 1.0 and precision of 0.99. Precision is less than 1.0 because priors of expected sequence length and sequence similarity scores--which are not implemented in orthofisher--resulted in more missing genes in the BUSCO pipeline than the orthofisher pipeline.
FAQ
I am having trouble installing orthofisher, what should I do?
Please install orthofisher using a virtual environment as described in the installation instructions. If you are still running into issues after installing in a virtual environment, please contact Jacob L. Steenwyk via email or twitter.
orthofisher is developed and maintained by Jacob Steenwyk
Owner
- Name: Jacob L. Steenwyk
- Login: JLSteenwyk
- Kind: user
- Location: Berkeley, CA
- Company: University of California, Berkeley
- Website: https://jlsteenwyk.com
- Twitter: JLSteenwyk
- Repositories: 10
- Profile: https://github.com/JLSteenwyk
Berkeley Science Fellow and Postdoctoral Scholar. Evolutionary genomics and software development.
GitHub Events
Total
- Watch event: 4
- Push event: 1
Last Year
- Watch event: 4
- Push event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jacob L. Steenwyk | j****k@g****m | 104 |
| dependabot[bot] | 4****] | 1 |
| Jacob L Steenwyk | j****k@J****l | 1 |
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 2
- Total pull requests: 13
- Average time to close issues: about 4 hours
- Average time to close pull requests: 4 months
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 0.54
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 11
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- Ptero64 (1)
- sumanthmutte (1)
Pull Request Authors
- dependabot[bot] (13)
- JLSteenwyk (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 260 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 21
- Total maintainers: 1
pypi.org: orthofisher
orthofisher
- Homepage: https://github.com/JLSteenwyk/orthofisher.git
- Documentation: https://orthofisher.readthedocs.io/
- License: mit
-
Latest release: 1.1.1
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- sphinx-autobuild * develop
- Pygments *
- Sphinx *
- sphinx_rtd_theme *
- alabaster ==0.7.12 develop
- babel ==2.9.0 develop
- certifi ==2020.12.5 develop
- chardet ==4.0.0 develop
- docutils ==0.16 develop
- idna ==2.10 develop
- imagesize ==1.2.0 develop
- jinja2 ==2.11.3 develop
- livereload ==2.6.3 develop
- markupsafe ==1.1.1 develop
- packaging ==20.9 develop
- pygments ==2.7.2 develop
- pyparsing ==2.4.7 develop
- pytz ==2021.1 develop
- requests ==2.25.1 develop
- six ==1.15.0 develop
- snowballstemmer ==2.1.0 develop
- sphinx ==3.2.1 develop
- sphinx-autobuild ==2020.9.1 develop
- sphinxcontrib-applehelp ==1.0.2 develop
- sphinxcontrib-devhelp ==1.0.2 develop
- sphinxcontrib-htmlhelp ==1.0.3 develop
- sphinxcontrib-jsmath ==1.0.1 develop
- sphinxcontrib-qthelp ==1.0.3 develop
- sphinxcontrib-serializinghtml ==1.1.4 develop
- tornado ==6.1 develop
- urllib3 ==1.26.4 develop
- alabaster ==0.7.12
- babel ==2.9.0
- certifi ==2020.12.5
- chardet ==4.0.0
- docutils ==0.16
- idna ==2.10
- imagesize ==1.2.0
- jinja2 ==2.11.3
- markupsafe ==1.1.1
- packaging ==20.9
- pygments ==2.7.2
- pyparsing ==2.4.7
- pytz ==2021.1
- requests ==2.25.1
- snowballstemmer ==2.1.0
- sphinx ==3.2.1
- sphinx-rtd-theme ==0.5.0
- sphinxcontrib-applehelp ==1.0.2
- sphinxcontrib-devhelp ==1.0.2
- sphinxcontrib-htmlhelp ==1.0.3
- sphinxcontrib-jsmath ==1.0.1
- sphinxcontrib-qthelp ==1.0.3
- sphinxcontrib-serializinghtml ==1.1.4
- urllib3 ==1.26.4
- biopython >=1.79
- cython *
- numpy >=1.19.5
- tqdm >=4.56.0
- JamesIves/github-pages-deploy-action releases/v3 composite
- actions/checkout master composite
- actions/setup-python master composite
- codecov/codecov-action v1.0.7 composite
- dschep/install-pipenv-action v1 composite