Mercurial > repos > idot > prop_venn

diff venner.py @ 0:8ea9b4e5a389

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author g2cmnty@test-web1.g2.bx.psu.edu
date Wed, 22 Jun 2011 03:28:25 -0400
parents
children cc6707a1e044
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/venner.py	Wed Jun 22 03:28:25 2011 -0400
@@ -0,0 +1,251 @@
+#!/usr/bin/env python
+'''
+Created on Jul 13, 2010
+
+Generates Venn diagram from 2 or three input files
+
+one could generate output file that for each row contain the segment
+i.e. A, B, AB, AmB, BmA
+
+@author: Ido M. Tamir
+'''
+from mako.template import Template
+from optparse import OptionParser
+import urllib,re,sys
+
+class Bunch:
+    def __init__(self, d):
+        for k, v in d.items():
+            if isinstance(v, dict):
+                v = Bunch(v)
+            self.__dict__[k] = v
+
+class VennFile():
+    def __init__(self, filePath, column, name):
+        self.filePath = filePath
+        self.column = column
+        cleanname = re.sub("/","",name)
+        self.name = urllib.quote(cleanname, safe="%/:=&?~#+!$,;'@()*[]")
+        self.dict = {}
+    def read(self):
+        dict = {}
+        lineNr = 0
+        for line in open( self.filePath, 'rb'):
+            key = line.split("\t")[self.column].strip()
+            linesList = dict.get(key, [])
+            linesList.append(line+"\t"+str(lineNr))
+            dict[key] = linesList
+            lineNr += 1
+        self.dict = dict
+        return self
+
+class Venn2:
+    def __init__(self, title, size, one, two):
+        self.one = one.read()
+        self.two = two.read()
+        self.title = title
+        self.size = size
+    
+    def toUrl(self):
+        one_keys = set(self.one.dict.keys())
+        two_keys = set(self.two.dict.keys())
+        
+        keys_one_i_two = one_keys.intersection(two_keys)
+       
+        total = len(one_keys) + len(two_keys)
+        sizes = [len(one_keys), len(two_keys), 0, len(keys_one_i_two)]
+        sizes = self.relSizes(sizes, total)
+        names = [self.one.name, self.two.name]
+        return self.url(total, sizes, names)
+  
+    def relSizes(self, sizes, total):
+        return map(lambda s: str(int(round((s/float(total) * 100)))), sizes)  
+
+    def url(self, total, sizes, names):
+        base = "http://chart.apis.google.com/chart?cht=v&chd=t:"
+        counts = ",".join(sizes)
+        titlep = "&chtt="+self.title
+        size = "&chs="+str(self.size)+"x"+str(self.size)
+        legend = "&chdl="+"|".join(names)
+        url = base+counts+titlep+size+legend
+        return url
+    
+    def toHtml(self):
+        one_keys = set(self.one.dict.keys())
+        two_keys = set(self.two.dict.keys())
+       
+        numbers = Bunch({
+        "one_keys" : len(set(self.one.dict.keys())),
+        "two_keys" : len(set(self.two.dict.keys())),
+        "one_only" : len(one_keys.difference(two_keys)),
+        "two_only" : len(two_keys.difference(one_keys)),
+        "one_i_two" : len(one_keys.intersection(two_keys)),
+        })
+            
+        template = """
+<html>
+  <head>
+     <title>Venn diagram ${title}</title>
+  </head>
+  <body>
+     <h3>${ title }</h3>
+     <div>
+        <img src="${ url }"/>
+     </div>
+     <div>
+        <table>
+           <tr><th>Segment</th><th>Count</th></tr>
+           <tr><td>${ one }</td><td>${ n.one_keys }</td></tr>
+           <tr><td>${ two }</td><td>${ n.two_keys }</td></tr>
+           <tr><td>${ one } \ ${ two }</td><td>${ n.one_only }</td></tr>
+           <tr><td>${ two } \ ${ one }</td><td>${ n.two_only }</td></tr>
+           <tr><td>${ one } &cap; ${ two }</td><td>${ n.one_i_two }</td></tr>
+        </table>
+     </div>
+  </body>
+</html>"""
+        result = Template(template).render(one=self.one.name, two=self.two.name, n=numbers, title=self.title, url=self.toUrl())
+        return(result)
+
+
+
+class Venn3(Venn2):
+    def __init__(self, title, size, one, two, three):
+        Venn2.__init__(self, title, size, one, two)
+        self.three = three.read()
+           
+    def toUrl(self):
+        one_keys = set(self.one.dict.keys())
+        two_keys = set(self.two.dict.keys())
+        three_keys = set(self.three.dict.keys())
+
+        keys_one_i_two = one_keys.intersection(two_keys)
+        keys_one_i_three = one_keys.intersection(three_keys)
+        keys_two_i_three = two_keys.intersection(three_keys)
+        keys_one_i_two_i_three = one_keys.intersection(two_keys).intersection(three_keys)
+        
+        total = len(one_keys)+len(two_keys)+len(three_keys)
+        sizes = [len(one_keys), len(two_keys), len(three_keys), len(keys_one_i_two), len(keys_one_i_three), len(keys_two_i_three), len(keys_one_i_two_i_three)]
+        sizes = self.relSizes(sizes, total)
+        names = [self.one.name, self.two.name, self.three.name]
+        return self.url(total, sizes, names)
+
+    def toHtml(self):
+        one_keys = set(self.one.dict.keys())
+        two_keys = set(self.two.dict.keys())
+        three_keys = set(self.three.dict.keys())
+        
+        xa = one_keys.intersection(two_keys)
+        xt = two_keys.intersection(three_keys)
+        xd = xt.difference(one_keys)
+        
+        numbers = Bunch({
+        "one_keys" : len(set(self.one.dict.keys())),
+        "two_keys" : len(set(self.two.dict.keys())),
+        "three_keys" : len(set(self.three.dict.keys())),
+        "one_only" : len(one_keys.difference(two_keys.union(three_keys))),
+        "two_only" : len(two_keys.difference(one_keys.union(three_keys))),
+        "three_only" : len(three_keys.difference(one_keys.union(two_keys))),
+        "one_two" : len(one_keys.intersection(two_keys).difference(three_keys)),
+        "one_three" : len(one_keys.intersection(three_keys).difference(two_keys)),
+        "two_three" : len(two_keys.intersection(three_keys).difference(one_keys)),
+        "one_i_two_i_three" : len(one_keys.intersection(two_keys).intersection(three_keys))
+        })
+            
+        template = """
+<html>
+  <head>
+     <title>Venn diagram ${title}</title>
+  </head>
+  <body>
+     <h3>${ title }</h3>
+     <div>
+        <img src="${ url }"/>
+     </div>
+     <div>
+        <table>
+           <tr><th>Segment</th><th>Count</th></tr>
+           <tr><td>${ one }</td><td>${ n.one_keys }</td></tr>
+           <tr><td>${ two }</td><td>${ n.two_keys }</td></tr>
+           <tr><td>${ three }</td><td>${ n.three_keys }</td></tr>
+           <tr><td>${ one } \ (${ two } &cup; ${ three })</td><td>${ n.one_only }</td></tr>
+           <tr><td>${ two } \ (${ one } &cup; ${ three})</td><td>${ n.two_only }</td></tr>
+           <tr><td>${ three } \ (${ one } &cup; ${ two })</td><td>${ n.three_only }</td></tr>
+           <tr><td>${ one } &cap; ${ two } \ ${ three } </td><td>${ n.one_two }</td></tr>
+           <tr><td>${ one } &cap; ${ three } \ ${ two } </td><td>${ n.one_three }</td></tr>
+           <tr><td>${ two } &cap; ${ three } \ ${ one } </td><td>${ n.two_three }</td></tr>
+           <tr><td>${ one } &cap; ${ two } &cap; ${ three }</td><td>${ n.one_i_two_i_three }</td></tr>
+        </table>
+     </div>
+  </body>
+</html>"""
+        result = Template(template).render(one=self.one.name, two=self.two.name, three=self.three.name, n=numbers, title=self.title, url=self.toUrl())
+        return(result)
+
+
+
+
+def main():
+        '''main worker func'''
+        parser = OptionParser()
+        parser.add_option( "--files", dest="filePaths", help="file paths delimited by ,")
+        parser.add_option( "--columns", dest="columns", help="0 based columnIndices delimited by ,")
+        parser.add_option( "--asNames", dest="asNames", help="names of the columns for pretty print")
+        parser.add_option( "--title", dest="title", help="title of plot")
+        parser.add_option( "--size", dest="size", help="size plot, default 300")
+        parser.add_option( "--outname", dest="outfileHtml", help="path of generated html file")
+        
+        (o, args) = parser.parse_args()
+        errors = []
+        if o.filePaths is None:
+            errors.append("please add required paths to files")
+        if o.columns is None:
+            errors.append( "please add required columns" )
+        if o.asNames is None:
+            errors.append( "please add required asNames")
+        if len(errors) > 0:
+            print("\n".join(errors))
+            sys.exit()
+        filePaths = o.filePaths.split(",")
+        columns = o.columns.split(",")
+        columns = map(int, columns)
+        asNames = o.asNames.split(",")
+        if len(errors) > 0 and ( len(filePaths) != len(columns) or len(columns) != len(asNames) ):
+            errors.append( "different length of filePaths, columns or names:" +o.columns+" "+" "+o.names+" "+o.filePaths )
+        title = ""
+        if o.title:
+            title = o.title
+        if o.outfileHtml is None:
+            errors.append( "please add outfile name for html" )
+        if len(filePaths) > 3:
+            errors.append( "can only compare up to three files was:"+str(len(filePaths)))
+        if len(filePaths) == 1:
+            errors.append( "just one file to compare does not make sense!")
+        if len(errors) > 0:
+            print("\n".join(errors))
+            sys.exit()
+        
+        size = "300"
+        if o.size:
+            size = o.size
+        
+        fileCount = len(filePaths)
+        if fileCount == 2:
+            venn = Venn2(title, size, VennFile(filePaths[0],columns[0],asNames[0]), VennFile(filePaths[1], columns[1], asNames[1]))
+        else:
+            venn = Venn3(title, size, VennFile(filePaths[0],columns[0],asNames[0]), VennFile(filePaths[1], columns[1], asNames[1]), VennFile(filePaths[2],columns[2],asNames[2]))
+        htmlText = venn.toHtml()
+        html = open(o.outfileHtml, 'w')
+        try:
+            html.write(htmlText)
+        finally:
+            html.close()
+
+               
+        
+        
+if __name__ == '__main__':
+      main()
+
+#$ python venner.py --files testFiles/fileA.tab,testFiles/fileB.tab --columns 1,1 --outname out.html --asNames As,Bs
+