added --overlap-thresh option and fixed issue #7

docs/modules.rst

@@ -52,6 +52,7 @@ This will save the results in the current working directory with a folder named
 	 "--bordercolors","Comma-separated list of matplotlib-valid colors for borders. E.g., --bordercolors=r,b,k"
 	 "-o, --output","Output folder path where results will be stored. Default is current working directory."
 	 "--save-overlaps","Save overlapping regions/names for all the combinations as bed/txt files. Default is ``False``"
+	 "--overlap-thresh", "Minimum threshold to save the overlapping regions/names as bed/txt. Default is ``1``"
 	 "--figtype","{pdf,svg,ps,tiff,png} Figure type for the plot. e.g. --figtype svg. Default is ``pdf``"
 	 "--figsize","Figure size as width and height.e.g. --figsize 12 12."
 	 "--fontsize","Font size for the plot labels. Default is ``14``"
@@ -105,6 +106,7 @@ This will save the results in the current working directory with a folder named
  	 "--bedtools-options","List any of the arguments available for bedtool’s intersect command. Type bedtools intersect --help to view all the options. For example: --bedtools-options f=0.8,r,etc"
 	 "-o, --output","Output folder path where plots will store. Default is current working directory."
 	 "--save-overlaps","Save overlapping regions/names for all the combinations as bed/txt files. Default is ``False``"
+	 "--overlap-thresh", "Minimum threshold to save the overlapping regions/names as bed/txt. Default is ``1``"
 	 "--order", "The order of intersections of sets {freq,degree}. e.g. --order degree. Default is ``freq`` "
 	 "--ninter", "Number of top intersections to plot. Default is ``30``"
 	 "--showzero", "Show empty overlap combinations. Default is ``False``"
@@ -119,7 +121,6 @@ This will save the results in the current working directory with a folder named
 	 "--scriptonly", "Set to generate Rscript only, if R/UpSetR package is not installed. Default is ``False``"
 	 "--showshiny", "Print the combinations of intersections to input to Shiny App. Default is ``False``"
 
-
 Pairwise intersection module
 ============================
 Once you have installed Intervene, you can type: 

intervene/__init__.py

@@ -1 +1 @@
-__version__ = '0.6.2'
+__version__ = '0.6.3'

intervene/intervene

@@ -21,6 +21,11 @@ from intervene import helpers
 from argparse import ArgumentParser, RawTextHelpFormatter
 import intervene
 
+import matplotlib
+#TrueType fonts for PostScript and PDF files
+matplotlib.rcParams['pdf.fonttype'] = 42
+matplotlib.rcParams['ps.fonttype'] = 42
+
 #main function
 def main():
 
@@ -66,6 +71,10 @@ def main():
                     help='Save overlapping regions/names for all the combinations as bed/txt. '
                        'Default is "%(default)s".\n\n')
 
+    venn_parser.add_argument('--overlap-thresh', dest='overlapthresh', type=int, default=1,
+                  help='Minimum threshold to save the overlapping regions/names as bed/txt. '
+                       'Default is: "%(default)s"\n\n')
+
     venn_parser.add_argument('--title', type=str, dest='title',
                   help='Title of the plot. '
                        'By default it is not set.\n\n') 
@@ -137,6 +146,10 @@ def main():
                     help='Save overlapping regions/names for all the combinations as bed/txt.'
                        'Default is "%(default)s".\n\n')
 
+    upset_parser.add_argument('--overlap-thresh', dest='overlapthresh', type=int, default=1,
+                  help='Minimum threshold to save the overlapping regions/names as bed/txt. '
+                       'Default is: "%(default)s"\n\n')
+
     upset_parser.add_argument('--project', type=str, default="Intervene",
                   help='Project name for the output. '
                        'Default is: "%(default)s"\n\n')  

intervene/modules/upset/upset.py

@@ -53,15 +53,16 @@ def genomic_upset(options, label_names):
 
         #save the intersected results
         if options.saveoverlaps:
-            file_name = ''
-            name_itr = 0
-            for name in t:
-                if name == '1':
-                    file_name += '_'+label_names[name_itr]
-                name_itr +=1
-            file_name = ''.join(t)+file_name
-            hlp.create_dir(output+'/sets')
-            x.moveto(output+'/sets/'+file_name+'.bed')
+            if X >= options.overlapthresh:
+                file_name = ''
+                name_itr = 0
+                for name in t:
+                    if name == '1':
+                        file_name += '_'+label_names[name_itr]
+                    name_itr +=1
+                file_name = ''.join(t)+file_name
+                hlp.create_dir(output+'/sets')
+                x.moveto(output+'/sets/'+file_name+'.bed')
 
         #delete all temp files
         helpers.cleanup()
@@ -95,17 +96,18 @@ def list_upset(options, label_names):
 
         #save the intersected results
         if options.saveoverlaps:
-            file_name = ''
-            name_itr = 0
-            for name in t:
-                if name == '1':
-                    file_name += '_'+label_names[name_itr]
-                name_itr +=1
-            file_name = ''.join(t)+file_name
-            hlp.create_dir(output+'/sets')
-            inter_file = open(output+'/sets/'+file_name+'.txt', 'w')
-            inter_file.writelines('\n'.join(list(X)))
-            inter_file.close()
+            if len(X) >= options.overlapthresh:
+                file_name = ''
+                name_itr = 0
+                for name in t:
+                    if name == '1':
+                        file_name += '_'+label_names[name_itr]
+                    name_itr +=1
+                file_name = ''.join(t)+file_name
+                hlp.create_dir(output+'/sets')
+                inter_file = open(output+'/sets/'+file_name+'.txt', 'w')
+                inter_file.writelines('\n'.join(list(X)))
+                inter_file.close()
 
     return(weights)
 

intervene/modules/venn/list_venn.py

@@ -8,6 +8,11 @@
 import matplotlib.patches as patches
 from matplotlib import colors
 import math
+import matplotlib
+
+#TrueType fonts for PostScript and PDF files
+matplotlib.rcParams['pdf.fonttype'] = 42
+matplotlib.rcParams['ps.fonttype'] = 42
 
 default_colors = [
     # r, g, b, a