Now a python package

Hoohm · Aug 2, 2018 · d41c552 · d41c552
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Showing 8 changed files with 44 additions and 1 deletion.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,3 @@
+dist*
+build*
+CITE_seq_Count*
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
 
+## [1.1] - 2018-08-02
+### Changed
+- Cite-seq-Count is now a python package!
+
 ## [0.2] - 2018-07-17
 ### Added
 - Compatibility with tags of different lengths

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -0,0 +1,7 @@
+Copyright 2018 Roelli Patrick
+
+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.
diff --git a/cite_seq_count/__init__.py b/cite_seq_count/__init__.py
diff --git a/CITE-seq-count.py → cite_seq_count/__main__.py b/CITE-seq-count.py → cite_seq_count/__main__.py
@@ -121,8 +121,9 @@ def parse_tags_csv(filename):
 
 def check_tags(ab_map, maximum_dist):
     ab_barcodes = ab_map.keys()
+    print(ab_barcodes)
     for a,b in combinations(ab_barcodes,2):
-        if(Levenshtein.hamming(a,b)<= maximum_dist):
+        if(Levenshtein.distance(a,b)<= maximum_dist):
             sys.exit('Minimum hamming distance of TAGS barcode is less than given threshold\nPlease use a smaller distance; exiting')
 
 

diff --git a/cite_seq_count/__pycache__/__init__.cpython-36.pyc b/cite_seq_count/__pycache__/__init__.cpython-36.pyc
diff --git a/cite_seq_count/__pycache__/__main__.cpython-36.pyc b/cite_seq_count/__pycache__/__main__.cpython-36.pyc
diff --git a/setup.py b/setup.py
@@ -0,0 +1,28 @@
+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="CITE-seq-Count",
+    version="1.1",
+    author="Roelli Patrick",
+    author_email="patrick.roelli@gmail.com",
+    description="A small python package that deals with counting CITE seq or hashing data for single cell",
+    url="https://github.com/Hoohm/CITE-seq-Count/",
+    packages=setuptools.find_packages(),
+    entry_points={
+          'console_scripts': [
+              'CITE-seq-Count = cite_seq_count.__main__:main'
+          ]
+      },
+    classifiers=(
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ),
+    install_requires=[
+          'regex>=2018.07.11',
+          'python-levenshtein>=0.12.0'
+      ]
+)