change to rst for PyPI
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Heng Li
parent
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include *.h
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include Makefile
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include ksw2_dispatch.c
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include getopt.c
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include main.c
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include README.md
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include python/minimap2.c
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include python/cminimap2.h
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include python/cminimap2.pxd
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include python/minimap2.pyx
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include python/README.md
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@ -1,43 +1,55 @@
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## Minimap2 Python Binding
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=======================
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Minimap2 Python Binding
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=======================
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[Minimap2][minimap2] is a fast and accurate pairwise aligner for genomic and
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transcribed nucleotide sequences. This module wraps minimap2 and provides a
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convenient interface to calling minimap2 in Python.
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`Minimap2 <https://github.com/lh3/minimap2>` is a fast and accurate pairwise
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aligner for genomic and transcribed nucleotide sequences. This module wraps
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minimap2 and provides a convenient interface to calling minimap2 in Python.
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### Installation
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Installation
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------------
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The minimap2 model can be installed directly with:
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```sh
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git clone https://github.com/lh3/minimap2
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cd minimap2
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python setup.py install
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```
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or with [pip][pip]:
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```sh
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pip install --user minimap2
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```
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### Usage
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.. code:: shell
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git clone https://github.com/lh3/minimap2
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cd minimap2
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python setup.py install
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or with pip:
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.. code:: shell
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pip install --user minimap2
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Usage
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-----
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The following Python program shows the key functionality of this module:
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```python
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import minimap2 as mm
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a = mm.Aligner("test/MT-human.fa")
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if not a: raise Exception("ERROR: failed to load/build index")
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for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
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print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
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```
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.. code:: python
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import minimap2 as mm
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a = mm.Aligner("test/MT-human.fa")
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if not a: raise Exception("ERROR: failed to load/build index")
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for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
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print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
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It builds an index from the specified sequence file (or loads an index if a
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pre-built index is supplied), aligns a sequence against it, traverses each hit
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and prints them out.
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### APIs
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APIs
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----
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#### Class minimap2.Aligner
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Class minimap2.Aligner
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~~~~~~~~~~~~~~~~~~~~~~
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.. code:: python
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Aligner(fn_idx_in, preset=None, ...)
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```python
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Aligner(fn_idx_in, preset=None, ...)
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```
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Arguments:
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* `fn_idx_in`: index or sequence file name. Minimap2 automatically tests the
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@ -67,13 +79,15 @@ Arguments:
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* `fn_idx_out`: name of file to which the index is written
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```python
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map(query_seq)
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```
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.. code:: python
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map(query_seq)
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This methods maps `query_seq` against the index. It *yields* a generator,
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generating a series of `Alignment` objects.
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#### Class minimap2.Alignment
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Class minimap2.Alignment
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~~~~~~~~~~~~~~~~~~~~~~~~
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This class has the following properties:
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@ -105,11 +119,7 @@ This class has the following properties:
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give the length and the operator of each CIGAR operation.
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An Alignment object can be converted to a string in the following format:
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```
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q_st q_en strand ctg ctg_len r_st r_en blen-NM blen mapq cg:Z:cigar_str
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```
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::
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[minimap2]: https://github.com/lh3/minimap2
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[pip]: https://pypi.python.org/pypi/pip
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q_st q_en strand ctg ctg_len r_st r_en blen-NM blen mapq cg:Z:cigar_str
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28
setup.py
28
setup.py
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@ -4,9 +4,17 @@ except ImportError:
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from distutils.core import setup
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from distutils.extension import Extension
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from Cython.Build import cythonize
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import sys
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cmdclass = {}
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try:
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from Cython.Build import build_ext
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except ImportError: # without Cython
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module_src = 'python/minimap2.c'
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else: # with Cython
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module_src = 'python/minimap2.pyx'
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cmdclass['build_ext'] = build_ext
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import sys
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sys.path.append('python')
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setup(
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@ -16,12 +24,16 @@ setup(
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description = 'Minimap2 python binding',
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author = 'Heng Li',
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author_email = 'lh3@me.com',
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license = 'MIT',
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keywords = ['bioinformatics', 'sequence-alignment'],
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ext_modules = cythonize([Extension('minimap2',
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['python/minimap2.pyx', 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c', 'kalloc.c',
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'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c', 'kthread.c', 'map.c',
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'misc.c', 'sdust.c', 'sketch.c'],
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ext_modules = [Extension('minimap2',
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sources = [module_src, 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c',
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'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
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'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c'],
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depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
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'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
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'python/cminimap2.h', 'python/cminimap2.pxd'],
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extra_compile_args = ['-msse4'], # WARNING: ancient x86_64 CPUs don't have SSE4
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include_dirs = ['.'],
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libraries = ['z', 'm', 'pthread'])])
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)
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libraries = ['z', 'm', 'pthread'])],
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cmdclass = cmdclass)
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