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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 def get_opt(data):
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11 return [('r','r',False),('c','c',False)]
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12
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13 def red(st,l):
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14 if len(st) <= l: return st
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15 l1,l2 = l/2,l/2
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16 return st[:l1]+".."+st[len(st)-l2:]
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17
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18 def get_row_names(data,t):
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19 if data == "": return []
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20 max_len =38
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21 fname = data.dataset.file_name
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22 opt = []
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23 rc = ''
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24 # lines = [(red(v.split()[0],max_len),'%s' % str(v.split()[0]),False) for i,v in enumerate(open(fname))]
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25 if t == 'b': lines = [(red(v.split()[0],max_len),'%d' % (i+1),False) for i,v in enumerate(open(fname)) if len(v.split()) > 3 ]
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26 else: lines = [(red(v.split()[0],max_len),'%d' % (i+1),False) for i,v in enumerate(open(fname))]
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27 return sorted(opt+lines)
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28
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29 def get_cols(data,t,c):
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30 if data == "": return []
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31 max_len =32
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32 fname = data.dataset.file_name
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33 opt = []
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34 if c != 'cl':
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35 opt.append(('no '+c,'%d' % -1,False))
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36 if t == 'c':
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37 rc = ''
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38 lines = [(red((rc+"#"+str(i+1)+":"+v[0]),max_len),'%d' % (i+1),False) for i,v in enumerate(zip(*[line.split() for line in open(fname)]))]
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39 else:
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40 rc = ''
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41 lines = [(red((rc+"#"+str(i+1)+":"+v.split()[0]),max_len),'%d' % (i+1),False) for i,v in enumerate(open(fname))]
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42 return opt+lines
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43
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44 """
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45 def get_phecols(i,addNone,hint):
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46 hint = hint.lower()
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47 fname = i.dataset.file_name
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48 try:
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49 f = open(fname,'r')
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50 except:
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51 return [('get_phecols unable to open file "%s"' % fname,'None',False),]
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52 header = f.next()
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53 h = header.strip().split()
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54 dat = [(x,'%d' % i,False) for i,x in enumerate(h)]
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55 matches = [i for i,x in enumerate(h) if x.lower().find(hint) <> -1]
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56 if len(matches) > 0:
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57 sel = matches[0]
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58 dat[sel] = (dat[sel][0],dat[sel][1],True)
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59 if addNone:
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60 dat.insert(0,('None - no Manhattan plot','0', False ))
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61 return dat
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62 """
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63
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64
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65 """
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66 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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67 outfile = 'out_html'
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68 job_name = param_dict.get( 'name', 'Manhattan QQ plots' )
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69 killme = string.punctuation + string.whitespace
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70 trantab = string.maketrans(killme,'_'*len(killme))
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71 newname = '%s.html' % job_name.translate(trantab)
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72 data = out_data[outfile]
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73 data.name = newname
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74 data.info='%s run at %s' % (job_name,timenow())
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75 out_data[outfile] = data
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76 app.model.context.flush()
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77 """
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