--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/plotting/venn_list.py	Mon May 06 14:05:13 2013 -0400
@@ -0,0 +1,135 @@
+#!/usr/bin/env python
+"""Plot up to 3-way Venn Diagram using R limma vennDiagram (via rpy)
+
+This script is copyright 2010 by Peter Cock, The James Hutton Institute
+(formerly SCRI), UK. All rights reserved.
+See accompanying text file for licence details (MIT/BSD style).
+
+This is version 0.0.3 of the script.
+"""
+
+
+import sys
+import rpy
+
+def stop_err(msg, error_level=1):
+    """Print error message to stdout and quit with given error level."""
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(error_level)
+
+try:
+    import rpy
+except ImportError:
+    stop_err("Requires the Python library rpy (to call R)")
+
+try:
+    rpy.r.library("limma")
+except:
+    stop_err("Requires the R library limma (for vennDiagram function)")
+
+
+if len(sys.argv)-1 not in [7, 10, 13]:
+    stop_err("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv)-1))
+
+all_file, all_type, all_label = sys.argv[1:4]
+set_data = []
+if len(sys.argv)-1 >= 7:
+    set_data.append(tuple(sys.argv[4:7]))
+if len(sys.argv)-1 >= 10:
+    set_data.append(tuple(sys.argv[7:10]))
+if len(sys.argv)-1 >= 13:
+    set_data.append(tuple(sys.argv[10:13]))
+pdf_file = sys.argv[-1]
+n = len(set_data)
+print "Doing %i-way Venn Diagram" % n
+
+def load_ids(filename, filetype):
+    if filetype=="tabular":
+        for line in open(filename):
+            if not line.startswith("#"):
+                yield line.rstrip("\n").split("\t",1)[0]
+    elif filetype=="fasta":
+        for line in open(filename):
+            if line.startswith(">"):
+                yield line[1:].rstrip("\n").split(None,1)[0]
+    elif filetype.startswith("fastq"):
+        #Use the Galaxy library not Biopython to cope with CS
+        from galaxy_utils.sequence.fastq import fastqReader
+        handle = open(filename, "rU")
+        for record in fastqReader(handle):
+            #The [1:] is because the fastaReader leaves the @ on the identifer.
+            yield record.identifier.split()[0][1:]
+        handle.close()
+    elif filetype=="sff":
+        try:
+            from Bio.SeqIO import index
+        except ImportError:
+            stop_err("Require Biopython 1.54 or later (to read SFF files)")
+        #This will read the SFF index block if present (very fast)
+        for name in index(filename, "sff"):
+            yield name
+    else:
+        stop_err("Unexpected file type %s" % filetype)
+
+def load_ids_whitelist(filename, filetype, whitelist):
+    for name in load_ids(filename, filetype):
+        if name in whitelist:
+            yield name
+        else:
+            stop_err("Unexpected ID %s in %s file %s" % (name, filetype, filename))
+
+if all_file in ["", "-", '""', '"-"']:
+    #Load without white list
+    sets = [set(load_ids(f,t)) for (f,t,c) in set_data]
+    #Take union
+    all = set()
+    for s in sets:
+        all.update(s)
+    print "Inferred total of %i IDs" % len(all)
+else:
+    all = set(load_ids(all_file, all_type))
+    print "Total of %i IDs" % len(all)
+    sets = [set(load_ids_whitelist(f,t,all)) for (f,t,c) in set_data]
+
+for s, (f,t,c) in zip(sets, set_data):
+    print "%i in %s" % (len(s), c)
+
+#Now call R library to draw simple Venn diagram
+try:
+    #Create dummy Venn diagram counts object for three groups
+    cols = 'c("%s")' % '","'.join("Set%i" % (i+1) for i in range(n))
+    rpy.r('groups <- cbind(%s)' % ','.join(['1']*n))
+    rpy.r('colnames(groups) <- %s' % cols)
+    rpy.r('vc <- vennCounts(groups)')
+    #Populate the 2^n classes with real counts
+    #Don't make any assumptions about the class order
+    #print rpy.r('vc')
+    for index, row in enumerate(rpy.r('vc[,%s]' % cols)):
+        if isinstance(row, int) or isinstance(row, float):
+            #Hack for rpy being too clever for single element row
+            row = [row]
+        names = all
+        for wanted, s in zip(row, sets):
+            if wanted:
+                names = names.intersection(s)
+            else:
+                names = names.difference(s)
+        rpy.r('vc[%i,"Counts"] <- %i' % (index+1, len(names)))
+    #print rpy.r('vc')
+    if n == 1:
+        #Single circle, don't need to add (Total XXX) line
+        names = [c for (t,f,c) in set_data]
+    else:
+        names = ["%s\n(Total %i)" % (c, len(s)) for s, (f,t,c) in zip(sets, set_data)]
+    rpy.r.assign("names", names)
+    rpy.r.assign("colors", ["red","green","blue"][:n])
+    rpy.r.pdf(pdf_file, 8, 8)
+    rpy.r("""vennDiagram(vc, include="both", names=names,
+                         main="%s", sub="(Total %i)",
+                         circle.col=colors)
+                         """ % (all_label, len(all)))
+    rpy.r.dev_off()
+except Exception, exc:
+    stop_err( "%s" %str( exc ) )
+rpy.r.quit( save="no" )
+print "Done"