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Fast pairwise sequence alignment using SeqAn, in Python.

• 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 abranch for SWIG 2)

Export the environment variableSEQAN_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 standardswig command, e.g. because it is calledswig3 or because it is not in thePATH, just export another environment variable calledSWIG, e.g.:

export SWIG=swig3

Now you can use one of the following methods to installseqanpy.

pip install seqanpy

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 yourPYTHONPATH.

To install to a specific folder, put your destination folderafter the --install-lib option. Remember to add that to yourPYTHONPATH

importseqanpyprint(seqanpy.align_global('ACCGGT','CCG'))