version 0.6.1

Author: Aziz Khan

docs/changelog.rst

@@ -0,0 +1,28 @@
+=========
+Changelog
+=========
+
+Version 0.6.1
+-------------
+Released date: December 16, 2017
+
+In this release, we have fixed various bugs and introduced new features:
+
+* Users now can provide all the `BedTools` options by setting `--bedtools-options` argument in `venn`, `upset` and `pairwise` module. Thanks to Issue #3
+* Now users can save all the overlapping genomic regions as BED and name lists as text file as by setting `--save-overlaps`. Thanks to those who suggested this feature.
+* We added `--bordercolors` to change the Venn border colors.
+
+
+Version 0.6.0
+-------------
+Released date: December 11, 2017
+
+* Fixed the pairwise module's `--names` argument. Thanks to @adomingues for reporting the bug.
+
+
+Version 0.5.9
+-------------
+Released date: December 08, 2017
+
+* Fixed the bug with two lists, issue #1 reported by @dayanne-castro
+* Fixed upset module memory issue for large number of sets

docs/conf.py

@@ -59,9 +59,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.5.8'
+version = '0.6.1'
 # The full version, including alpha/beta/rc tags.
-release = 'v0.5.8'
+release = 'v0.6.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -42,4 +42,4 @@ Welcome to Intervene - a tool for intersection and visualization of multiple gen
    shinyapp
    support
    cite
-   
+   changelog

docs/modules.rst

@@ -3,6 +3,7 @@ Intervene modules
 =================
 Intervene provides three types of plots to visualize intersections of genomic regions and list sets. These are pairwise heatmap of N genomic region sets, classic Venn diagrams of genomic regions and list sets of up to 6-way and UpSet plots.
 
+.. note:: By default the intersection genomic regions is computed using default parameters of `BedTools`. Intervene version > v0.6.0 now allows users to provide all the arguments available in BedTools' commands  by using **--bedtools-options**.
 
 Venn diagram module 
 ===================
@@ -42,12 +43,15 @@ This will save the results in the current working directory with a folder named
    :widths: 10, 80
 
      "-h, --help","To show the help message and exit"
-	 "-i","Input genomic regions in (BED/GTF/GFF) format or lists of genes/SNPs IDs. For files in a directory use *.<extension>. e.g. *.bed"
+	 "-i, --input","Input genomic regions in (BED/GTF/GFF) format or lists of genes/SNPs IDs. For files in a directory use *.<extension>. e.g. *.bed"
 	 "--type","{genomic,list}. Type of input sets. Genomic regions or lists of genes/SNPs. Default is ``genomic``"
 	 "--names","Comma-separated list of names as labels for input files. If it is not set file names will be used as labels. For example: --names=A,B,C,D,E,F"
-	 "--filenames","Use file names as labels instead. Default is ``False``"             
-	 "--colors","Comma-separated list of matplotlib-valid colors. E.g., --colors=r,b,k"
+	 "--filenames","Use file names as labels instead. Default is ``False``"
+	 "--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"
+	 "--colors","Comma-separated list of matplotlib-valid colors for fill. E.g., --colors=r,b,k"
+	 "--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``"
 	 "--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``"
@@ -98,7 +102,9 @@ This will save the results in the current working directory with a folder named
 	 "--type","Type of input sets. Genomic regions or lists of genes sets {genomic,list}. Default is ``genomic``"  
  	 "--names","Comma-separated list of names as labels for input files. If it is not set file names will be used as labels. For example: --names=A,B,C,D,E,F"
  	 "--filenames","Use file names as labels instead. Default is ``True``"
+ 	 "--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``"
 	 "--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``"
@@ -113,7 +119,7 @@ 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: 
@@ -152,7 +158,7 @@ This will save the results in the current working directory with a folder named
    :widths: 10, 80
 
 	  "-h, --help","show this help message and exit"
-	  "-i","Input genomic regions in (BED/GTF/GFF) format. For files in a directory use *.<extension>. e.g. *.bed"
+	  "-i, --input","Input genomic regions in (BED/GTF/GFF) format. For files in a directory use *.<extension>. e.g. *.bed"
 	  "--type","{genomic,list}. Type of input sets. Genomic regions or lists of genes/SNPs. Default is ``genomic``"
 	  "--compute","Compute count/fraction of overlaps or statistical relationships. {``count``, ``frac``, ``jaccard``, ``fisher``, ``reldist``}"
 	  " ","--compute=count - calculates the number of overlaps."
@@ -161,6 +167,7 @@ This will save the results in the current working directory with a folder named
 	  " ","--compute=reldist - calculate the distribution of relative distances. `Read more details here <http://bedtools.readthedocs.io/en/latest/content/tools/reldist.html>`_"
 	  " ","--compute=fisher - calculate Fisher`s statistic. `Read more details here <http://bedtools.readthedocs.io/en/latest/content/tools/fisher.html>`_"
 	  " ","Note: For jaccard and reldist regions should be pre-shorted or set --sort``"
+	  "--bedtools-options","List any of the arguments available for bedtool’s subcommands: interset, jaccard, fisher, reldist. Type `bedtools <subcommand> --help` to view all the options. For example: --bedtools-options f=0.8,r,etc"
 	  "--corr","Compute the correlation. By default set to False"
 	  "--corrtype","Select the type of correlation from ``pearson``, ``kendall`` or ``spearman``."
 	  " ","--corrtype=pearson: computes the Pearson correlation. (Default)"

intervene/__init__.py

@@ -1 +1 @@
-__version__ = '0.6.0'
+__version__ = '0.6.1'

intervene/helpers.py

@@ -35,6 +35,28 @@ def venn_order(input_files):
 
     return len(input_files)
 
+def map_bedtools_options(bedtools_options):
+    '''
+    Create a dict of bedtools intersect options
+    '''
+    
+    kwargs = {}
+    
+    try:
+        for args in bedtools_options.split(','):
+            args = args.split('=')
+            if len(args) > 1:
+                if args[1] in ['true','True']:
+                    kwargs[args[0]]= True
+                else:
+                    kwargs[args[0]]= args[1]
+            else:
+                kwargs[args[0]]= True
+    except:
+        pass  
+    
+    return kwargs
+
 def get_filenames(input_files):
     """
     Checks the venn-type
@@ -183,6 +205,23 @@ def default_colors():
 
     return default_colors
 
+def default_border_colors():
+    """
+    Get a list of RGBA colors 
+    """
+
+    default_colors = [
+        # r, g, b, a
+        [0, 0, 0, 1],
+        [0, 0, 0, 1],
+        [0, 0, 0, 1],
+        [0, 0, 0, 1],
+        [0, 0, 0, 1],
+        [0, 0, 0, 1],
+    ]
+
+    return default_colors
+
 def get_colors(color_list):
     """
     Get color combinations for Venn diagram. This converts color names to RGBA