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comparison venner.py @ 1:cc6707a1e044 draft default tip

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added fixes from Brad Langhorst; https://bitbucket.org/account/notifications/read/3443176/patch-for-proportional-venn-tool-in-galaxy; added tool_dependencies for Mako template untested
author Ido Tamir <ido.tamir@imp.ac.at>
date Mon, 24 Sep 2012 16:46:21 +0200
parents 8ea9b4e5a389
children
comparison
equal deleted inserted replaced
0:8ea9b4e5a389 1:cc6707a1e044
25 self.filePath = filePath 25 self.filePath = filePath
26 self.column = column 26 self.column = column
27 cleanname = re.sub("/","",name) 27 cleanname = re.sub("/","",name)
28 self.name = urllib.quote(cleanname, safe="%/:=&?~#+!$,;'@()*[]") 28 self.name = urllib.quote(cleanname, safe="%/:=&?~#+!$,;'@()*[]")
29 self.dict = {} 29 self.dict = {}
30
30 def read(self): 31 def read(self):
31 dict = {} 32 dict = {}
32 lineNr = 0 33 lineNr = 0
33 for line in open( self.filePath, 'rb'): 34 for line in open( self.filePath, 'rb'):
34 key = line.split("\t")[self.column].strip() 35 key = line.split("\t")[self.column].strip()
86 <html> 87 <html>
87 <head> 88 <head>
88 <title>Venn diagram ${title}</title> 89 <title>Venn diagram ${title}</title>
89 </head> 90 </head>
90 <body> 91 <body>
91 <h3>${ title }</h3>
92 <div> 92 <div>
93 <img src="${ url }"/> 93 <img src="${ url }"/>
94 </div> 94 </div>
95 <div> 95 <div>
96 <table> 96 <table>
97 <tr><th>Segment</th><th>Count</th></tr> 97 <tr><th>Set</th><th>Count</th></tr>
98 <tr><td>${ one }</td><td>${ n.one_keys }</td></tr> 98 <tr><td>${ one }</td><td>${ n.one_keys }</td></tr>
99 <tr><td>${ two }</td><td>${ n.two_keys }</td></tr> 99 <tr><td>${ two }</td><td>${ n.two_keys }</td></tr>
100 <tr><td>${ one } \ ${ two }</td><td>${ n.one_only }</td></tr> 100 <tr><td>${ one } \ ${ two }</td><td>${ n.one_only }</td></tr>
101 <tr><td>${ two } \ ${ one }</td><td>${ n.two_only }</td></tr> 101 <tr><td>${ two } \ ${ one }</td><td>${ n.two_only }</td></tr>
102 <tr><td>${ one } &cap; ${ two }</td><td>${ n.one_i_two }</td></tr> 102 <tr><td>${ one } &cap; ${ two }</td><td>${ n.one_i_two }</td></tr>
103 </table> 103 </table>
104 </div> 104 </div>
105 </body> 105 </body>
106 </html>""" 106 </html>"""
107 result = Template(template).render(one=self.one.name, two=self.two.name, n=numbers, title=self.title, url=self.toUrl()) 107 result = Template(template).render(one=urllib.unquote(self.one.name), two=urllib.unquote(self.two.name), n=numbers, title=self.title, url=self.toUrl())
108 return(result) 108 return(result)
109 109
110 110
111 111
112 class Venn3(Venn2): 112 class Venn3(Venn2):
156 <html> 156 <html>
157 <head> 157 <head>
158 <title>Venn diagram ${title}</title> 158 <title>Venn diagram ${title}</title>
159 </head> 159 </head>
160 <body> 160 <body>
161 <h3>${ title }</h3>
162 <div> 161 <div>
163 <img src="${ url }"/> 162 <img src="${ url }"/>
164 </div> 163 </div>
165 <div> 164 <div>
166 <table> 165 <table>
167 <tr><th>Segment</th><th>Count</th></tr> 166 <tr><th>Set</th><th>Count</th></tr>
168 <tr><td>${ one }</td><td>${ n.one_keys }</td></tr> 167 <tr><td>${ one }</td><td>${ n.one_keys }</td></tr>
169 <tr><td>${ two }</td><td>${ n.two_keys }</td></tr> 168 <tr><td>${ two }</td><td>${ n.two_keys }</td></tr>
170 <tr><td>${ three }</td><td>${ n.three_keys }</td></tr> 169 <tr><td>${ three }</td><td>${ n.three_keys }</td></tr>
171 <tr><td>${ one } \ (${ two } &cup; ${ three })</td><td>${ n.one_only }</td></tr> 170 <tr><td>${ one } \ (${ two } &cup; ${ three })</td><td>${ n.one_only }</td></tr>
172 <tr><td>${ two } \ (${ one } &cup; ${ three})</td><td>${ n.two_only }</td></tr> 171 <tr><td>${ two } \ (${ one } &cup; ${ three})</td><td>${ n.two_only }</td></tr>
177 <tr><td>${ one } &cap; ${ two } &cap; ${ three }</td><td>${ n.one_i_two_i_three }</td></tr> 176 <tr><td>${ one } &cap; ${ two } &cap; ${ three }</td><td>${ n.one_i_two_i_three }</td></tr>
178 </table> 177 </table>
179 </div> 178 </div>
180 </body> 179 </body>
181 </html>""" 180 </html>"""
182 result = Template(template).render(one=self.one.name, two=self.two.name, three=self.three.name, n=numbers, title=self.title, url=self.toUrl()) 181 result = Template(template).render(one=urllib.unquote(self.one.name), two=urllib.unquote(self.two.name), three=urllib.unquote(self.three.name), n=numbers, title=self.title, url=self.toUrl())
183 return(result) 182 return(result)
184 183
185 184
186 185
187 186