Since the time of writing Heng Li, the author of minimap2, has provided a python binding in the minimap2 source and at https://pypi.python.org/pypi/mappy. Users are strongly encouraged to use Heng's python library rather that the version presented here. Despite its short life, the latter will be no longer supported out of deference to Heng's version.
Python bindings to minimap2 aligner; sufficient to load and index and perform
alignments of sequences to the index to obtain basic statistics.
These python bindings are licensed under Mozilla Public License 2.0, minimap is licenced The MIT License.
Documentation can be found at https://nanoporetech.github.io/minimappy/.
The git source repository contains minimap2 as a submodule. The repository should therefore be cloned using the recursive option.
The package setup.py script requires libminimap2.a to have been built in the
submodule directory before running. This can be performed via the libminimap2.a
target. To build and install the package one should
therefore run:
git clone --recursive https://github.com/nanoporetech/minimappy.git
make minimap2/libminimap2.a
python setup.py install
The MinimapAligner class provides a pythonic interface to minimap2 aligner.
It takes as input a minimap index or .fasta reference on construction and can
then be used to find alignments of sequences given as strings:
from minimappy import MinimapAligner
index = 'path/to/index' # the path given to minimap2 index
seq = 'ACGATCGCGATCGA'
aligner = MinimapAligner(index)
alignments = aligner.align_seq(seq)
print('Found {} alignments.'.format(len(alignments))
for aln in alignments:
print(' ', aln)The alignments are returned as a named tuple, e.g.:
Alignment(rname='yeast', orient='+', pos=0, mapq=60, cigar='915M3D29M3D27M3D13M', NM=12, flags=0)Alignment parameters can be given as they are on the minimap2 command line:
from minimappy import MinimapAligner
index = 'path/to/index'
options = '-ax map10k'
aligner = MinimapAligner(index, options=options)