htswfrontend/htswfrontend/htsw_reports/reports.py

   1 from htswfrontend.exp_track.models import *
   2 from django.http import HttpResponse
   3 from django.core.exceptions import ObjectDoesNotExist
   4 from django.shortcuts import render_to_response, get_object_or_404
   5
   6 badLibBgColor = '#cccccc'
   7 def getBgColor(reads_cnt,exp_type,isBadLib):
   8   if isBadLib: return badLibBgColor
   9   # Color Scheme: green is more than 12M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds are ~ double
  10   bgcolor = '#ffcdd0'  # Red is the color for minimum read counts
  11   rc_thr = [12000000,5000000,3000000] # Default for ChIP-Seq and Methyl-Seq
  12   if exp_type == 'RNA-seq':
  13     rc_thr = [20000000,10000000,6000000]
  14
  15   if reads_cnt > rc_thr[0]:
  16     bgcolor = '#66ff66'  # Green
  17   else:
  18     if reads_cnt > rc_thr[1]:
  19       bgcolor ='#00ccff'  # Blue
  20     else:
  21        if reads_cnt > rc_thr[2]:
  22          bgcolor ='#ffcc33'  # Orange
  23   #tstr = '<div style="background-color:'+bgcolor+';color:black">'
  24   #tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
  25   #tstr += '</div>'
  26
  27   return bgcolor
  28
  29 def report1(request):
  30   if not request.user.is_authenticated():
  31     str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
  32     return render_to_response('htsw_reports/report.html',{'main':str})
  33
  34   EXP = 'ChIP-seq'
  35
  36   if request.has_key('aflid'):
  37     AFL_Id = request['aflid']
  38     try:
  39       AFL = Affiliation.objects.get(id=AFL_Id).name
  40       AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
  41     except ObjectDoesNotExist:
  42       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_Id+"'")
  43   else:
  44     AFL = 'ENCODE_Tier1'
  45     AFL_CNT = ''
  46     try:
  47       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
  48     except ObjectDoesNotExist:
  49       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
  50
  51   if request.user.username == 'caltech':
  52     if AFL.find('ENCODE') < 0:  return HttpResponse('Record Not Found <div style="margin-right:20px"><a target=_self href="/admin" target=_self>HOME</a></div>')
  53
  54   TFall = Library.objects.values('antibody').order_by('antibody').distinct()
  55   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
  56
  57   TFs = TFall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
  58   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
  59
  60   # Check Replicate numbers
  61   Reps = 1
  62   RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
  63   if len(RepRecs) > 0: Reps = RepRecs[0].replicate
  64
  65   ########
  66   str = ''
  67   str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">HOME</a></span>'
  68   ##str += '<span style="margin-right:20px">Max Replicates: '+MaxRep.replicate.__str__()+'</span>'
  69   str += '<span>Select another <b>'+EXP+'</b> Report:</span>  <select onchange="window.location=\'/htsw_reports/report?aflid=\'+this.options[selectedIndex].value; return false;">'
  70
  71   if request.user.username == 'caltech':
  72     Affil_List = Affiliation.objects.filter(name__contains='ENCODE').distinct()
  73   else:
  74     Affil_List = Affiliation.objects.distinct()
  75
  76   for af in Affil_List:
  77     str += '<option value='+af.id.__str__()
  78     if AFL_Id == af.id.__str__():
  79       str += ' selected'
  80     str += '>'+af.name+' '+af.contact+'</option>'
  81   str += '</select>'
  82
  83   str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 12 M</span><span style="margin-left:5px;background-color:#00ccff"> >  5 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 3 M</span><span style="margin-left:5px;background-color:#ffcdd0"> < 3 M</span><span style="margin-left:5px;background-color:'+badLibBgColor+'">Bad Library</span></span>'
  84
  85   str += '<span style="margin-left:20px">'
  86   str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
  87   str += '  | '
  88   str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
  89
  90   bgc = '#ffffff'
  91   pbgc = '#f7f7f7'
  92   str += '<br/><br/><table border=1>'
  93   str += '<tr><th style="text-align:right">PROJECT</th><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+' <span style="font-size:140%">'+EXP+'</span></th></tr>'
  94   str += '<tr><th style="text-align:right">CELL LINE</th>'
  95   for H in CLLs:
  96     str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
  97     tbgc = bgc
  98     bgc = pbgc
  99     pbgc = tbgc
 100   str += '</tr><tr><th style="text-align:left">TF</th>'
 101   bgc = '#ffffff'
 102   pbgc = '#f7f7f7'
 103   for H in CLLs:
 104     for r in range(1,Reps+1):
 105       str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
 106     tbgc = bgc
 107     bgc = pbgc
 108     pbgc = tbgc
 109   str += '</tr>'
 110   str += '<tr><td align=right><a title="View Libraries Records" target=_self href=/admin/fctracker/library/?affiliations__id__exact='+AFL_Id+'&experiment_type__exact=INPUT_RXLCh>Total Chromatin</a></td>'
 111   bgc = '#ffffff'
 112   pbgc = '#f7f7f7'
 113   for H in CLLs:
 114     for r in range(1,Reps+1):
 115       repReads = Library.objects.filter(experiment_type='INPUT_RXLCh',affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),replicate=r)
 116       str += "<td align=center style='background-color:"+bgc+"'>"
 117       if len(repReads) == 0:
 118         str += 'No Libraries'
 119       else:
 120         cnt = 0
 121         for R1 in repReads:
 122           rres = R1.aligned_m_reads()
 123           # Check data sanlty
 124           if rres[2] != 'OK':
 125             str += '<div style="border:solid red 2px">'+rres[2]
 126           else:
 127             cnt = rres[1]
 128             if cnt > 0:
 129               str += "<div style='background-color:"+getBgColor(cnt,EXP,(R1.libtags().find('Bad library')!=-1))+";font-size:140%'>"
 130               str += "%1.2f" % (cnt/1000000.0)+" M"
 131             else:  str += "<div style='background-color:#ffcdd0;width:100%;font-size:140%'>0 Reads"
 132           str += "<div style='font-size:70%'><a title='View Library Record' target=_self style='font-weight:bold;color:black' href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+"</a>, "+R1.condition.nickname
 133           if R1.libtags().find('Data submitted to DCC') != -1:
 134             str += "<div style='border:solid #666666 1px;'>data submitted</div>"
 135           str += "</div>"
 136           str += "</div>"
 137       str += '</td>'
 138     tbgc = bgc
 139     bgc = pbgc
 140     pbgc = tbgc
 141   str += '</tr>'
 142
 143   for T in TFs:
 144     str += '<tr>'
 145     try:
 146       if T['antibody']:
 147         str += '<td><a title="View Libraries Records" target=_self href=/admin/fctracker/library/?affiliations__id__exact='+AFL_Id+'&antibody__id__exact='+T['antibody'].__str__()+'>'+Antibody.objects.get(id=T['antibody']).nickname+'</a></td>'
 148     except Antibody.DoesNotExist:
 149       str += '<td>n/a</td>'
 150
 151     bgc = '#ffffff'
 152     pbgc = '#f7f7f7'
 153     for H in CLLs:
 154       for r in range(1,Reps+1):
 155         repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),antibody=T['antibody'].__str__(),replicate=r)
 156         str += "<td align=center style='background-color:"+bgc+"'>"
 157         if len(repReads) == 0:
 158           str += 'No Libraries'
 159         else:
 160           cnt = 0
 161           for R1 in repReads:
 162             rres = R1.aligned_m_reads()
 163             # Check data sanity
 164             if rres[2] != 'OK':
 165               str += '<div style="border:solid red 2px">'+rres[2]
 166             else:
 167               cnt = rres[1]
 168               if cnt > 0:
 169                 str += "<div style='background-color:"+getBgColor(cnt,EXP,(R1.libtags().find('Bad library')!=-1))+";font-size:140%;margin:2px'>"
 170                 str += "%1.2f" % (cnt/1000000.0)+" M"
 171               else:  str += "<div style='background-color:#ffcdd0;width:100%;font-size:140%'>0 Reads"
 172             str += "<div style='font-size:70%'><a title='View Library Record' target=_self style='font-weight:bold;color:black' href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+"</a>, "+R1.condition.nickname
 173             if R1.libtags().find('Data submitted to DCC') != -1:
 174               str += "<div style='border:solid #666666 1px;'>data submitted</div>"
 175             str += "</div>"
 176             str += "</div>"
 177         str += '</td>'
 178       tbgc = bgc
 179       bgc = pbgc
 180       pbgc = tbgc
 181     str += '</tr>'
 182   str += '</table>'
 183
 184   return render_to_response('htsw_reports/report.html',{'main': str})
 185
 186
 187 def report_RM(request): #for RNA-Seq and Methyl-Seq
 188   if not request.user.is_authenticated():
 189     str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
 190     return render_to_response('htsw_reports/report.html',{'main':str})
 191
 192   EXP = 'RNA-seq'
 193
 194   if request.has_key('exp'):
 195     EXP = request['exp'] # Methyl-seq
 196
 197   if request.has_key('aflid'):
 198     AFL_Id = request['aflid']
 199     try:
 200       AFL = Affiliation.objects.get(id=AFL_Id).name
 201       AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
 202     except ObjectDoesNotExist:
 203       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_Id+"'")
 204   else:
 205     AFL = 'ENCODE_Tier1'
 206     AFL_CNT = ''
 207     try:
 208       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
 209     except ObjectDoesNotExist:
 210       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
 211
 212   if request.user.username == 'caltech':
 213     if AFL.find('ENCODE') < 0:  return HttpResponse('Record Not Found <div style="margin-right:20px"><a target=_self href="/admin" target=_self>HOME</a></div>')
 214
 215   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
 216   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
 217
 218   ########
 219   # Check Replicate numbers
 220   Reps = 1
 221   RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
 222   if len(RepRecs) > 0: Reps = RepRecs[0].replicate
 223
 224   str = ''
 225   str += '<span style="margin-right:20px"><a  target=_self href="/admin" target=_self" style="font-size:140%">HOME</a></span>'
 226   str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select onchange="window.location=\'/htsw_reports/report_RM?exp='+EXP+'&aflid=\'+this.options[selectedIndex].value; return false;">'
 227
 228   if request.user.username == 'caltech':
 229     Affil_List = Affiliation.objects.filter(name__contains='ENCODE').distinct()
 230   else:
 231     Affil_List = Affiliation.objects.distinct()
 232
 233   for af in Affil_List:
 234     str += '<option value='+af.id.__str__()
 235     if AFL_Id == af.id.__str__():
 236       str += ' selected'
 237     str += '>'+af.name+' '+af.contact+'</option>'
 238   str += '</select>'
 239
 240   if EXP == 'RNA-seq':
 241     str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 20 M</span><span style="margin-left:5px;background-color:#00ccff"> >  10 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 6 M</span><span style="margin-left:5px;background-color:#ffcdd0"> < 6 M</span><span style="margin-left:5px;background-color:'+badLibBgColor+'">Bad Library</span></span>'
 242     str += '<span style="margin-left:20px">'
 243     str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report?exp=RNA-seq&aflid='+AFL_Id+'"><b>ChIP-Seq</b> Report</a>'
 244     str += '  | '
 245     str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
 246   else:
 247     str += '<span style="margin-left:20px;padding:1px;border:solid #cccccc 1px">color scheme: <span style="margin-left:5px;background-color:#66ff66"> > 12 M</span><span style="margin-left:5px;background-color:#00ccff"> >  5 M</span><span style="margin-left:5px;background-color:#ffcc33"> > 3 M</span><span style="margin-left:5px;background-color:#ffcdd0"> < 3 M</span><span style="margin-left:5px;background-color:'+badLibBgColor+'">Bad Library</span></span>'
 248     str += '<span style="margin-left:20px">'
 249     str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/htsw_reports/report?exp=RNA-seq&aflid='+AFL_Id+'"><b>ChIP-Seq</b> Report</a>'
 250     str += '  | '
 251     str += '<a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
 252
 253   str += '<br/><br/><table border=1>'
 254   str += '<tr><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+'  <span style="font-size:140%">'+EXP+'</span></th></tr>'
 255   str += '<tr>'
 256   bgc = '#ffffff'
 257   pbgc = '#f7f7f7'
 258   for H in CLLs:
 259     str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
 260     tbgc = bgc
 261     bgc = pbgc
 262     pbgc = tbgc
 263   str += '</tr><tr>'
 264   bgc = '#ffffff'
 265   pbgc = '#f7f7f7'
 266   for H in CLLs:
 267     for r in range(1,Reps+1):
 268       str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
 269     tbgc = bgc
 270     bgc = pbgc
 271     pbgc = tbgc
 272   str += '</tr>'
 273
 274   str += '<tr>'
 275   bgc = '#ffffff'
 276   pbgc = '#f7f7f7'
 277   for H in CLLs:
 278     for r in range(1,Reps+1):
 279       repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'],replicate=r)
 280       str += "<td align=center valign=top style='background-color:"+bgc+"'>"
 281       if len(repReads) == 0:
 282         str += 'No Libraries'
 283       else:
 284         cnt = 0
 285         for R1 in repReads:
 286           rres = R1.aligned_m_reads()
 287           # Check data sanlty
 288           if rres[2] != 'OK':
 289             str += '<div style="border:solid red 2px">'+rres[2]
 290           else:
 291             cnt = rres[1]
 292             if cnt > 0:
 293               str += "<div style='background-color:"+getBgColor(cnt,EXP,(R1.libtags().find('Bad library')!=-1))+";border:solid #cccccc 1px;font-size:140%'>"
 294               str += "%1.2f" % (cnt/1000000.0)+" M"
 295             else:  str += "<div style='background-color:#ffcdd0;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
 296           str += "<div style='font-size:80%'><a title='View Record' style='color:black' target=_self href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+"</a>, "+R1.condition.nickname+", "+R1.library_species.common_name+"</div>"
 297           str += "<div style='font-size:70%'>\""+R1.library_name+"\""
 298           if R1.libtags().find('Data submitted to DCC') != -1:
 299             str += "<div style='width:75%;border:solid #666666 1px;'>data submitted</div>"
 300           str += "</div>"
 301           str += "</div>"
 302       str += '</td>'
 303     tbgc = bgc
 304     bgc = pbgc
 305     pbgc = tbgc
 306   str += '</tr>'
 307   str += '</table>'
 308
 309   return render_to_response('htsw_reports/report.html',{'main': str})
 310
 311 def getNotRanFCs(request):
 312   if not request.user.is_authenticated():
 313     str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
 314     return render_to_response('htsw_reports/report.html',{'main':str})
 315
 316   FCall = FlowCell.objects.order_by('-run_date').distinct()
 317   str = '<table><tr><th>FlowCell</th><th>Lanes</th><th>Creation Date</th></tr>'
 318   for f in FCall:
 319     try:
 320       t = DataRun.objects.get(fcid=f.id)
 321     except ObjectDoesNotExist:
 322       str += '<tr><td>'+f.flowcell_id+'</td><td>'+f.Lanes()+'</td><td>'+f.run_date.__str__()+'</td></tr>'
 323   str += "</table>"
 324   return render_to_response('htsw_reports/report.html',{'main':str})
 325
 326 def test_Libs(request):
 327   if not request.user.is_authenticated():
 328     str= '<span style="margin-right:20px"><a target=_self href="/admin" target=_self style="font-size:140%">Please log in first</a></span>'
 329     return render_to_response('htsw_reports/report.html',{'main':str})
 330
 331   str = ''
 332   str += '<table border=1><tr><th>Lib ID</th><th>Current Libaray Name (Free Text)</th><th>Auto-composed Libaray Name (antibody + celline + libid + species + [replicate])</th></tr>'
 333   allLibs = Library.objects.all()
 334   #allLibs = Library.objects.filter(antibody__isnull=False)
 335   for L in allLibs:
 336     str += '<tr>'
 337     str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
 338     str += '<td>'
 339     str += L.experiment_type+'_'
 340     if L.cell_line.cellline_name != 'Unknown':
 341       str += L.cell_line.cellline_name+'_'
 342
 343     try:
 344       if L.antibody is not None:
 345         str += L.antibody.nickname + '_'
 346     except Antibody.DoesNotExist:
 347       pass
 348
 349     str += 'Rep'+L.replicate.__str__()
 350     str += '</td></tr>'
 351
 352   str += '</table>'
 353   return HttpResponse(str)