initial commit

README.rst

@@ -13,11 +13,17 @@ Installation
 Intervene requires the following Python modules and R packages:
 
 	* Python (=> 2.7 ): https://www.python.org/
+	* BedTools (Latest version): https://github.com/arq5x/bedtools2
 	* pybedtools (>= 0.7.9): https://daler.github.io/pybedtools/
 	* Pandas (>= 0.16.0): http://pandas.pydata.org/
 	* R (>= 3.0): https://www.r-project.org/
 	* R packages including UpSetR, corrplot
 
+Install BEDTools
+-----------------
+We are using pybedtools, which is Python wraper of BEDTools. So, BEDTools is should be installed before using Intervene.It's recomended to have a latest version, but if you have an older version already install. Please read the instructions at https://github.com/arq5x/bedtools2 to install BEDTolls, and make sure the bedtools is on your path and you are able to call it from any directory.
+
+
 Install required Python modules
 -------------------------------
 If you already have a working installation of Python, the easiest way to install required Python modules is by using ``pip``. If you're setting up Python for the first time, we recommend to install it using Anaconda Python distribution http://continuum.io/downloads. These come with several helpful scientific and data processing libraries. These are available for platforms including Windows, Mac OSX and Linux.
@@ -38,7 +44,6 @@ or using conda
 
 Read more details about ''pybedtools'' installation: https://daler.github.io/pybedtools/main.html
 
-
 **Install Pandas**
 
 Install it from PyPi
@@ -53,7 +58,6 @@ Or install with conda
 
 	conda install pandas
 
-
 **Install argparser**
 
 .. code-block:: bash

docs/install.rst

@@ -7,11 +7,16 @@ Intervene requires the following Python modules and R packages:
 
 
 	* Python (=> 2.7 ): https://www.python.org/
+	* BedTools (Latest version): https://github.com/arq5x/bedtools2
 	* pybedtools (>= 0.7.9): https://daler.github.io/pybedtools/
 	* Pandas (>= 0.16.0): http://pandas.pydata.org/
 	* R (>= 3.0): https://www.r-project.org/
 	* R packages including UpSetR, corrplot
 
+Install BEDTools
+-----------------
+We are using pybedtools, which is Python wraper of BEDTools. So, BEDTools is should be installed before using Intervene.It's recomended to have a latest version, but if you have an older version already install. Please read the instructions at https://github.com/arq5x/bedtools2 to install BEDTolls, and make sure the bedtools is on your path and you are able to call it from any directory.
+
 Install required Python modules
 -------------------------------
 
@@ -33,7 +38,6 @@ or using conda
 
 Read more details about ''pybedtools'' installation: https://daler.github.io/pybedtools/main.html
 
-
 **Install Pandas**
 
 Install it from PyPi
@@ -48,7 +52,6 @@ Or install with conda
 
 	conda install pandas
 
-
 **Install argparser**
 
 .. code-block:: bash

intervene/__init__.py

@@ -1 +1 @@
-__version__ = '0.39'
+__version__ = '0.4.0'

intervene/modules/upset/upset.py

@@ -16,7 +16,6 @@ def create_r_script(labels, names, options):
     """
     It create an Rscript for UpSetR plot for the genomic regions.
 
-
     """
     #temp_f = tempfile.NamedTemporaryFile(delete=False)
     #temp_f = open(tempfile.mktemp(), "w")
@@ -26,18 +25,17 @@ def create_r_script(labels, names, options):
     output_name = options.output+'/'+'intervene_'+options.type+'_UpSet_plot.'+options.figtype
 
     temp_f.write('#!/usr/bin/env Rscript'+"\n")
+    temp_f.write('if (suppressMessages(!require("UpSetR"))) suppressMessages(install.packages("UpSetR", repos="http://cran.us.r-project.org"))\n')
     temp_f.write('library("UpSetR")\n')
-
 
     if options.figtype == 'pdf':
-        temp_f.write(options.figtype+'("'+output_name+'", width='+str(options.figsize[0])+', height='+str(options.figsize[1])+')'+'\n')
+        temp_f.write(options.figtype+'("'+output_name+'", width='+str(options.figsize[0])+', height='+str(options.figsize[1])+', onefile=FALSE)'+'\n')
 
     elif options.figtype == 'ps':
         temp_f.write('postscript("'+output_name+'", width='+str(options.figsize[0])+', height='+str(options.figsize[1])+')'+'\n')
-
     else:
         temp_f.write(options.figtype+'("'+output_name+'", width='+str(options.dpi*options.figsize[0])+', height='+str(options.dpi*options.figsize[1])+', res='+str(options.dpi)+')\n')
-
+     
     temp_f.write("expressionInput <- c(")
 
     last = 1