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change to rst for PyPI

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Heng Li
2017-09-16 22:29:52 -04:00
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python/README.md → python/README.rst
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@@ -1,43 +1,55 @@
## Minimap2 Python Binding
=======================
Minimap2 Python Binding
=======================
[Minimap2][minimap2] is a fast and accurate pairwise aligner for genomic and
transcribed nucleotide sequences. This module wraps minimap2 and provides a
convenient interface to calling minimap2 in Python.
`Minimap2 <https://github.com/lh3/minimap2>` is a fast and accurate pairwise
aligner for genomic and transcribed nucleotide sequences. This module wraps
minimap2 and provides a convenient interface to calling minimap2 in Python.
### Installation
Installation
------------
The minimap2 model can be installed directly with:
```sh
git clone https://github.com/lh3/minimap2
cd minimap2
python setup.py install
```
or with [pip][pip]:
```sh
pip install --user minimap2
```
### Usage
.. code:: shell
git clone https://github.com/lh3/minimap2
cd minimap2
python setup.py install
or with pip:
.. code:: shell
pip install --user minimap2
Usage
-----
The following Python program shows the key functionality of this module:
```python
import minimap2 as mm
a = mm.Aligner("test/MT-human.fa")
if not a: raise Exception("ERROR: failed to load/build index")
for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
```
.. code:: python
import minimap2 as mm
a = mm.Aligner("test/MT-human.fa")
if not a: raise Exception("ERROR: failed to load/build index")
for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
It builds an index from the specified sequence file (or loads an index if a
pre-built index is supplied), aligns a sequence against it, traverses each hit
and prints them out.
### APIs
APIs
----
#### Class minimap2.Aligner
Class minimap2.Aligner
~~~~~~~~~~~~~~~~~~~~~~
.. code:: python
Aligner(fn_idx_in, preset=None, ...)
```python
Aligner(fn_idx_in, preset=None, ...)
```
Arguments:
* `fn_idx_in`: index or sequence file name. Minimap2 automatically tests the
@@ -67,13 +79,15 @@ Arguments:
* `fn_idx_out`: name of file to which the index is written
```python
map(query_seq)
```
.. code:: python
map(query_seq)
This methods maps `query_seq` against the index. It *yields* a generator,
generating a series of `Alignment` objects.
#### Class minimap2.Alignment
Class minimap2.Alignment
~~~~~~~~~~~~~~~~~~~~~~~~
This class has the following properties:
@@ -105,11 +119,7 @@ This class has the following properties:
give the length and the operator of each CIGAR operation.
An Alignment object can be converted to a string in the following format:
```
q_st q_en strand ctg ctg_len r_st r_en blen-NM blen mapq cg:Z:cigar_str
```
::
[minimap2]: https://github.com/lh3/minimap2
[pip]: https://pypi.python.org/pypi/pip
q_st q_en strand ctg ctg_len r_st r_en blen-NM blen mapq cg:Z:cigar_str