seqanpy
Fast pairwise sequence alignment using SeqAn, in Python.
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.5%) to scientific vocabulary
Keywords
Repository
Fast pairwise sequence alignment using SeqAn, in Python.
Basic Info
Statistics
- Stars: 13
- Watchers: 3
- Forks: 7
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Fast pairwise sequence alignment using SeqAn, in Python.
REQUIREMENTS
- Python 2.7 or 3.3+.
- A C++ 11 compiler, e.g. GCC 4.8+. If you are using SeqAn 2.2+ (see below), then you need a C++ 14 compiler, e.g. GCC 5.2+.
- SeqAn 1.4 or later. If you are using SeqAn 2.2+, then you need a C++ 14 compiler, e.g. GCC 5.2+.
- SWIG 3 (there is a branch for SWIG 2)
INSTALL
Export the environment variable SEQAN_INCLUDE_PATH to the parent folder of your seqan include folder. For instance, if your SeqAn headers are in /usr/local/include/seqan, set:
sh
export SEQAN_INCLUDE_PATH=/usr/local/include
If your SWIG 3 is not executed by the standard swig command, e.g. because it is called swig3 or because it is not in the PATH, just export another environment variable called SWIG, e.g.:
sh
export SWIG=swig3
Now you can use one of the following methods to install seqanpy.
Pip
sh
pip install seqanpy
Setup.py (development version)
Clone the github repo. To install system-wide:
sh
python2.7 setup.py install
To install in the current folder:
sh
python2.7 setup.py install --install-lib .
Remember to add the current folder to your PYTHONPATH.
To install to a specific folder, put your destination folder
after the --install-lib option. Remember to add that to your
PYTHONPATH
USAGE
python
import seqanpy
print(seqanpy.align_global('ACCGGT', 'CCG'))
Owner
- Name: Fabio Zanini
- Login: iosonofabio
- Kind: user
- Location: Sydney, Australia
- Company: UNSW Sydney
- Website: https://fabilab.org
- Twitter: fabiousername
- Repositories: 24
- Profile: https://github.com/iosonofabio
Physics, bioinformatics, virology, evolution, data science, and bioengineering. I usually code in Python, C++, and Javascript.
GitHub Events
Total
Last Year
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Fabio Zanini | f****i@t****e | 20 |
| Fabio Zanini | f****i@f****m | 18 |
| Colin Anthony | c****1@g****m | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 2
- Average time to close issues: 28 minutes
- Average time to close pull requests: 10 days
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 3.0
- Average comments per pull request: 3.5
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- rneher (1)
Pull Request Authors
- ColinAnthony (1)
- mdcao (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 6 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 1
- Total maintainers: 1
pypi.org: seqanpy
Fast pairwise sequence alignment using SeqAn
- Homepage: https://github.com/iosonofabio/seqanpy
- Documentation: https://seqanpy.readthedocs.io/
- License: BSD/2-clause
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Latest release: 0.2
published over 8 years ago