Merge pull request #17 from fossilfriend/master

PyPI packaging + updated readme + bin directory with executable

README.md

@@ -83,7 +83,13 @@ python setup.py install --user
 
 #### Quick Start
 
-iterativeWGCNA can be run without installing the iterativeWGCNA package by excuting the wrapper script `run_iterative_wgcna.py` in the iterativeWGCNA directory. At a minimum, the `-i` option (`--inputFile`) denoting the full path to the input file must be specified.
+If installed via the `pip` or `easy_install`, iterativeWGCNA can be run using the `iterativeWGCNA` command.  At minimum, the `-i` option (`--inputFile`) denoting the full path to the input file must be specified:
+
+```sh
+iterativeWGCNA -i <input_file_path>
+```
+
+iterativeWGCNA can also be run without installing the iterativeWGCNA package by executing the wrapper script `run_iterative_wgcna.py` in the iterativeWGCNA directory. At a minimum, the `-i` option (`--inputFile`) denoting the full path to the input file must be specified:
 
 ```sh
 python run_iterative_wgcna.py -i <input_file_path> 

bin/iterativeWGCNA

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+
+'''Convenience wrapper for running iterativeWGCNA directly from source tree.'''
+
+# Installation workaround - see README
+# import readline
+
+from iterativeWGCNA.cmlargs import parse_command_line_args
+from iterativeWGCNA.iterativeWGCNA import IterativeWGCNA
+
+if __name__ == '__main__':
+    cmlArgs = parse_command_line_args()
+    alg = IterativeWGCNA(cmlArgs)
+    alg.run()
+
+__author__ = 'Emily Greenfest-Allen'
+__copyright__ = 'Copyright 2016, University of Pennsylvania'

build/lib/iterativeWGCNA/__main__.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python2.7
+"""
+Perform iterative WGCNA analysis
+
+python dependencies:
+  * rpy2
+  * matplotlib
+
+R dependencies:
+  * WGCNA
+"""
+
+from .cmlargs import parse_command_line_args
+from .iterativeWGCNA import IterativeWGCNA
+
+if __name__ == '__main__':
+    args = parse_command_line_args()
+    alg = IterativeWGCNA(args)
+    alg.run()
+
+__author__ = 'Emily Greenfest-Allen'
+__copyright__ = 'Copyright 2016, University of Pennsylvania'

build/lib/iterativeWGCNA/analysis.py

@@ -0,0 +1,18 @@
+'''
+functions in support of data analysis
+'''
+
+# TODO move to RManager or wgcnaManager
+
+from .r.imports import wgcna, stats, base
+
+def calculate_kME(expr, eigengene, calculateP):
+    '''
+    calculates eigengene connectivity
+    between an eigengene and expression data set
+    '''
+    if calculateP:
+        correlation = wgcna().corAndPvalue(base().t(expr), base().t(eigengene))
+    else:
+        correlation = base().as_data_frame(stats().cor(base().t(expr), base().t(eigengene)))
+    return correlation