Add README, improve setup.py

LICENSE.txt

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2020 David Prihoda
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

README.md

@@ -1 +1,57 @@
-# usearchmap
+# USUM: Plotting sequence similarity using USEARCH & UMAP
+
+USUM uses [USEARCH](https://drive5.com/usearch/) and [UMAP](https://github.com/lmcinnes/umap) to plot DNA 🧬and protein 🧶 sequence similarity embeddings.
+
+![PyPI - Downloads](https://img.shields.io/pypi/dm/deepbgc.svg?color=green&label=PyPI%20downloads)
+[![PyPI license](https://img.shields.io/pypi/l/deepbgc.svg)](https://pypi.python.org/pypi/deepbgc/)
+[![PyPI version](https://badge.fury.io/py/deepbgc.svg)](https://badge.fury.io/py/deepbgc)
+
+## Installation
+
+Install `UCLUST` manually: https://drive5.com/usearch/download.html (consider supporting the author by buying the 64bit license)
+
+Install `usum` using PIP:
+
+```bash
+pip install usum
+```
+
+## Usage
+
+### Minimal example
+
+```bash
+usum sequences.fa --maxdist 0.2 --termdist 0.3 --output umap
+```
+
+### Multiple input files with labels
+
+```bash
+usum first.fa second.fa --labels First Second --maxdist 0.2 --termdist 0.3 --output umap
+```
+
+This will produce a PNG plot:
+
+![UMAP static example](docs/example1.png?raw=true "UMAP static example")
+
+An interactive [Bokeh](https://bokeh.org) HTML plot is also created:
+
+![UMAP Bokeh example](docs/example2.png?raw=true "UMAP Bokeh example")
+
+### Programmatic use
+
+```python
+from usum import usum
+
+# Show help
+help(usum)
+
+# Run USUM
+usum(inputs=['input.fa'], output='usum', maxdist=0.2, termdist=0.3)
+```
+
+## How it works
+
+- A sparse distance matrix is calculated using USEARCH [calc_distmx](https://drive5.com/usearch/manual/cmd_calc_distmx.html) command. 
+- The distance matrix is embedded as `precomputed` metric using [UMAP](https://github.com/lmcinnes/umap) 
+- The embedding is plotted using [umap.plot](https://umap-learn.readthedocs.io/en/latest/plotting.html).

setup.py

@@ -1,14 +1,35 @@
 from setuptools import setup
+import os
+
+about = {}
+# Read version number from deepbgc.__version__.py (see PEP 396)
+here = os.path.abspath(os.path.dirname(__file__))
+with open(os.path.join(here, 'usum', '__version__.py'), encoding='utf-8') as f:
+    exec(f.read(), about)
+
+# Read contents of readme file into string
+with open(os.path.join(here, 'README.md'), encoding='utf-8') as f:
+    long_description = f.read()
 
 setup(
-    name='usearchmap',
-    packages=['usearchmap'],
+    name='usum',
+    packages=['usum'],
+    version=about['__version__'],
+    description='USUM: Plotting sequence similarity using USEARCH & UMAP',
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    author='David Příhoda',
+    author_email='[email protected]',
+    license='MIT',
+    python_requires=">=3.6",
+    keywords='dna, protein, sequence, similarity, umap, usearch, uclust, plot',
+    url='https://github.com/prihoda/usum',
     install_requires=[
         'biopython',
         'umap-learn[plot]'
     ],
     entry_points={
-        'console_scripts': ['usearchmap = usearchmap.main:main']
+        'console_scripts': ['usum = usum.main:main']
     }
 )
 

usum/__init__.py

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+from .__version__ import __version__
+from .main import usum

usum/__version__.py

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+__version__ = '0.1.1'