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:

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.:

export SWIG=swig3

Now you can use one of the following methods to install seqanpy.

Pip

pip install seqanpy

Setup.py (development version)

Clone the github repo. To install system-wide:

python2.7 setup.py install

To install in the current folder:

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

import seqanpy
print(seqanpy.align_global('ACCGGT', 'CCG'))