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51 lines
1.5 KiB
Python
51 lines
1.5 KiB
Python
from galaxy import datatypes,model
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import sys,string,time
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def timenow():
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"""return current time as a string
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"""
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return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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def get_phecols(i,addNone,hint):
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"""
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return a list of phenotype columns for a multi-select list
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"""
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hint = hint.lower()
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fname = i.dataset.file_name
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try:
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f = open(fname,'r')
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except:
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return [('get_phecols unable to open file "%s"' % fname,'None',False),]
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header = f.next()
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h = header.strip().split()
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dat = [(x,'%d' % i,False) for i,x in enumerate(h)]
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matches = [i for i,x in enumerate(h) if x.lower().find(hint) <> -1]
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if len(matches) > 0:
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sel = matches[0]
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dat[sel] = (dat[sel][0],dat[sel][1],True)
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if addNone:
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dat.insert(0,('None - no Manhattan plot','0', False ))
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return dat
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def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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"""Sets the name of the data
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<outputs>
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<data format="pdf" name="allqq" />
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<data format="pdf" name="lowqq" parent="allqq"/>
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</outputs>
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"""
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outfile = 'out_html'
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job_name = param_dict.get( 'name', 'Manhattan QQ plots' )
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killme = string.punctuation + string.whitespace
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trantab = string.maketrans(killme,'_'*len(killme))
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newname = '%s.html' % job_name.translate(trantab)
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data = out_data[outfile]
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data.name = newname
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data.info='%s run at %s' % (job_name,timenow())
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out_data[outfile] = data
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app.model.context.flush()
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