add setup.py

ficusss · Jan 17, 2018 · 9002d49 · 9002d49
1 parent 7d96de0
commit 9002d49
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diff --git a/README.rst b/README.rst
diff --git a/pygmn/__init__.py b/pygmn/__init__.py
@@ -0,0 +1,8 @@
+# __init__.py
+
+from normalizations import total_count_normalization
+from normalizations import percentile_normalization
+from normalizations import quartile_normalization
+from normalizations import tmm_normalization
+
+__version__ = "0.1"
diff --git a/pygmn/normalizations.py b/pygmn/normalizations.py
@@ -3,6 +3,7 @@
 from scipy.stats import rankdata
 from utils import percentile
 
+#===============================================================================
 
 def total_count_normalization(matrix):
     """
@@ -20,6 +21,7 @@ def total_count_normalization(matrix):
     """
     return matrix / matrix.sum(axis=0)
 
+#===============================================================================
 
 def percentile_normalization(matrix, p):
     """
@@ -39,6 +41,7 @@ def percentile_normalization(matrix, p):
     """
     return matrix / percentile(matrix, p)
 
+#===============================================================================
 
 def quartile_normalization(matrix, q):
     """
@@ -63,6 +66,7 @@ def quartile_normalization(matrix, q):
     assert q in d, 'Unexpected quartile for normalization: "' + str(q) + '"'
     return percentile_normalization(matrix, d[q])
 
+#===============================================================================
 
 def tmm_normalization(matr, index_ref=None, trim_fold_change=0.3, trim_abs_expr=0.05):
     """
@@ -137,3 +141,5 @@ def log2_tmm(index_vec):
     # calculation tmm_factor and normalization of input data
     tmm_factor = 2 ** np.array([log2_tmm(i) for i in range(matrix.shape[1])])
     return matr / tmm_factor
+
+#===============================================================================
diff --git a/setup.py b/setup.py
@@ -0,0 +1,34 @@
+# setup.py
+
+
+PACKAGE = "pygmn"
+NAME = "pygmn"
+DESCRIPTION = "Package with methods for normalization matrices of genes expression."
+AUTHOR = "Grigory Feoktistov"
+AUTHOR_EMAIL = "[email protected]"
+URL = "https://github.com/ficusss/PyGMNormalize"
+VERSION = __import__(PACKAGE).__version__
+
+
+setup(
+    name=NAME,
+    version=VERSION,
+    description=DESCRIPTION,
+    long_description=read("README.md"),
+    author=AUTHOR,
+    author_email=AUTHOR_EMAIL,
+    license="BSD",
+    url=URL,
+    packages=find_packages(exclude=["tests.*", "tests"]),
+    package_data=find_package_data(PACKAGE, only_in_packages=False),
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "Environment :: Web Environment",
+        "Intended Audience :: Developers",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: OS Independent",
+        "Programming Language :: Python",
+        "Framework :: Django",
+    ],
+    zip_safe=False,
+)