Changed structure to PyPi package

.gitignore

@@ -1 +1,5 @@
 *.pyc
+build/
+dist/
+*.egg
+*.egg-info

CHANGES

@@ -1,3 +1,10 @@
+## 1.2.1 (2017-09-07)
+
+- Rearranged package structure towards a full Pypi packages
+- Renamed summary.R to utils/uropa_summary.R
+- Renamed reformat_output.R to utisl/uropa_reformat_output.R
+- Reflected changes in documentation
+
 ## 1.2.0 (2017-09-05)
 
 - Added an UpSetR plot to summary.R to cancel the need for Vennerable R package

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2016 MPI for Heart and Lung Research
+
+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.

MANIFEST.in

@@ -0,0 +1,2 @@
+include README.md
+include LICENSE

setup.py

@@ -0,0 +1,25 @@
+from setuptools import setup
+
+def readme():
+    with open('README.md') as f:
+        return f.read()
+
+setup(name='uropa',
+      version='1.2.1',
+      description='UROPA is a command line based tool, intended for genomic region annotation',
+      long_description=readme(),
+      url='https://github.molgen.mpg.de/loosolab/UROPA',
+      author='Jens Preussner',
+      author_email='jens.preussner@mpi-bn.mpg.de',
+      license='MIT',
+      packages=['uropa'],
+      entry_points = {
+        'console_scripts': ['uropa = uropa.uropa:main']
+      },
+      scripts = ['utils/uropa_summary.R', 'utils/uropa_reformat_output.R', 'utils/uropa2gtf.R'],
+      install_requires=[
+        'numpy',
+        'pysam'
+      ],
+      zip_safe=False,
+      include_package_data=True)

uropa/config.py

@@ -11,48 +11,47 @@
 def howtoconfig():
     """Defines the epilog that is given when help is requested."""
     epilog = dedent("""\
-	UROPA is a peak annotation tool facilitating the analysis of next-generation sequencing methods for
-	chromatin biology, like ChIPseq or ATACseq. There are already different peak annotation tools, like
-	HOMER or ChIPpeakAnno, but the advantage of UROPA is, that it can easily be fitted to your requirements.
-	UROPA was developed as an open source analysis pipeline for peaks generated from any peak caller.
+    UROPA is a peak annotation tool facilitating the analysis of next-generation sequencing methods for
+    chromatin biology, like ChIPseq or ATACseq. There are already different peak annotation tools, like
+    HOMER or ChIPpeakAnno, but the advantage of UROPA is, that it can easily be fitted to your requirements.
+    UROPA was developed as an open source analysis pipeline for peaks generated from any peak caller.
 
     Please cite upon usage:
-    Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M.
-    UROPA: a tool for Universal RObust Peak Annotation.
+    Kondili M, Fust A, Preussner J, Kuenne C, Braun T and Looso M. UROPA: A tool for Universal RObust Peak Annotation.
     Scientific Reports 7 (2017), doi: 10.1038/s41598-017-02464-y
 
-	All parameters and paths to input or output files should be reported in a JSON configuration file.
-	The configuration file should at least contain paths for bed and GTF files:
-
-	{
-	"queries": [],
-	"bed": "/path/to/bed/file.bed",
-	"gtf": "/path/to/annotation/file.gtf"
-	}
-
-	Different query types can be defined using the queries key:
-
-	{
-	"queries": [
-	  {...},
-	  {...}],
-	"bed": "/path/to/bed/file.bed",
-	"gtf": "/path/to/annotation/file.gtf"
-	}
-
-	Optionally, the priority key can be used to fine tune UROPAs behaviour:
-
-	{
-	"queries": [
-	  {...},
-	  {...}],
-	"bed": "/path/to/bed/file.bed",
-	"gtf": "/path/to/annotation/file.gtf",
-	"priority": "True"
-	}
-
-	Please visit http://uropa-manual.readthedocs.io/config.html for detailed information on configuration.
-	""")
+    All parameters and paths to input or output files should be reported in a JSON configuration file.
+    The configuration file should at least contain paths for bed and GTF files:
+
+    {
+    "queries": [],
+    "bed": "/path/to/bed/file.bed",
+    "gtf": "/path/to/annotation/file.gtf"
+    }
+
+    Different query types can be defined using the queries key:
+
+    {
+    "queries": [
+      {...},
+      {...}],
+    "bed": "/path/to/bed/file.bed",
+    "gtf": "/path/to/annotation/file.gtf"
+    }
+
+    Optionally, the priority key can be used to fine tune UROPAs behaviour:
+
+    {
+    "queries": [
+      {...},
+      {...}],
+    "bed": "/path/to/bed/file.bed",
+    "gtf": "/path/to/annotation/file.gtf",
+    "priority": "True"
+    }
+
+    Please visit http://uropa-manual.readthedocs.io/config.html for detailed information on configuration.
+    """)
     return epilog
 
 

uropa.py → uropa/uropa.py

@@ -1,10 +1,9 @@
-#!/usr/bin/env python
 """
 uropa.py: UROPA - Universal RObust Peak Annotator
 
 @authors: Maria Kondili, Jens Preussner and Annika Fust
 @license: MIT
-@version: 1.2.0
+@version: 1.2.1
 @maintainer: Mario Looso
 @email: mario.looso@mpi-bn.mpg.de
 """
@@ -26,14 +25,14 @@
 
 import numpy as np
 
-import uropa.config as cfg
-import uropa.overlaps as ovls
-import uropa.annotation as ant
-
-if __name__ == "__main__":
+import config as cfg
+import overlaps as ovls
+import annotation as ant
 
+#if __name__ == "__main__":
+def main():
     parser = argparse.ArgumentParser(
-        prog="uropa.py",
+        prog="uropa",
         description='UROPA - Universal RObust Peak Annotator.',
         epilog=cfg.howtoconfig(),
         formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -95,7 +94,7 @@
         "--version",
         help="prints the version and exits",
         action="version",
-        version="%(prog)s 1.2.0")
+        version="%(prog)s 1.2.1")
     args = parser.parse_args()
 
     config = args.input
@@ -345,7 +344,7 @@
     if args.reformat and len(queries) > 1 and not pr:
         logger.info("Reformatting output...")
         R_reform_Best = [
-            'reformat_output.R',
+            'uropa_reformat_output.R',
             '-i',
             besthits_outfile,
             '-k',
@@ -370,7 +369,7 @@
     #
     if args.summary:
         logger.info("Creating the Summary graphs of the results...")
-        summary_script = "summary.R"
+        summary_script = "uropa_summary.R"
         summary_output = outdir + "summary.pdf"
 
         if len(queries) > 1 and not pr and os.path.exists(merged_outfile):