Mercurial > repos > xuebing > sharplabtool

comparison tools/rgenetics/rgManQQ_code.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 from galaxy import datatypes,model
2 import sys,string,time
3
4
5 def timenow():
6 """return current time as a string
7 """
8 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
9
10
11 def get_phecols(i,addNone,hint):
12 """
13 return a list of phenotype columns for a multi-select list
14 """
15 hint = hint.lower()
16 fname = i.dataset.file_name
17 try:
18 f = open(fname,'r')
19 except:
20 return [('get_phecols unable to open file "%s"' % fname,'None',False),]
21 header = f.next()
22 h = header.strip().split()
23 dat = [(x,'%d' % i,False) for i,x in enumerate(h)]
24 matches = [i for i,x in enumerate(h) if x.lower().find(hint) <> -1]
25 if len(matches) > 0:
26 sel = matches[0]
27 dat[sel] = (dat[sel][0],dat[sel][1],True)
28 if addNone:
29 dat.insert(0,('None - no Manhattan plot','0', False ))
30 return dat
31
32
33 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
34 """Sets the name of the data
35 <outputs>
36 <data format="pdf" name="allqq" />
37 <data format="pdf" name="lowqq" parent="allqq"/>
38 </outputs>
39 """
40 outfile = 'out_html'
41 job_name = param_dict.get( 'name', 'Manhattan QQ plots' )
42 killme = string.punctuation + string.whitespace
43 trantab = string.maketrans(killme,'_'*len(killme))
44 newname = '%s.html' % job_name.translate(trantab)
45 data = out_data[outfile]
46 data.name = newname
47 data.info='%s run at %s' % (job_name,timenow())
48 out_data[outfile] = data
49 app.model.context.flush()
50