https://github.com/iosonofabio/seqanpy
Fast pairwise sequence alignment using SeqAn, in Python.
https://github.com/iosonofabio/seqanpy
pairwise-alignment python python-wrapper seqan sequence-alignment swig
Last synced: 2 months ago
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Fast pairwise sequence alignment using SeqAn, in Python.
- Host: GitHub
- URL: https://github.com/iosonofabio/seqanpy
- Owner: iosonofabio
- License: other
- Created: 2014-11-03T09:56:37.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2019-03-23T18:56:22.000Z (over 6 years ago)
- Last Synced: 2025-03-27T02:51:18.236Z (3 months ago)
- Topics: pairwise-alignment, python, python-wrapper, seqan, sequence-alignment, swig
- Language: C++
- Homepage:
- Size: 32.2 KB
- Stars: 13
- Watchers: 3
- Forks: 7
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[](https://travis-ci.org/iosonofabio/seqanpy)
[](https://pypi.org/project/seqanpy)
Fast pairwise sequence alignment using SeqAn, in Python.
# REQUIREMENTS
- [Python](https://www.python.org/) 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](http://www.seqan.de/) 1.4 or later. If you are using SeqAn 2.2+, then you need a C++ 14 compiler, e.g. GCC 5.2+.
- [SWIG](http://www.swig.org/) 3 (there is a [branch](https://github.com/iosonofabio/seqanpy/tree/swig2) 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'))
```