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