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 def getBgColor(reads_cnt,exp_type):
   7   # 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
   8   bgcolor = '#ff3300'  # Red is the color for minimum read counts
   9   rc_thr = [12000000,5000000,3000000] # Default for ChIP-Seq and Methyl-Seq
  10   if exp_type == 'RNA-seq':
  11     rc_thr = [20000000,10000000,6000000]
  12
  13   if reads_cnt > rc_thr[0]:
  14     bgcolor = '#66ff66'  # Green
  15   else:
  16     if reads_cnt > rc_thr[1]:
  17       bgcolor ='#00ccff'  # Blue
  18     else:
  19        if reads_cnt > rc_thr[2]:
  20          bgcolor ='#ffcc33'  # Orange
  21   #tstr = '<div style="background-color:'+bgcolor+';color:black">'
  22   #tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
  23   #tstr += '</div>'
  24
  25   return bgcolor
  26
  27 def report1(request):
  28   EXP = 'ChIP-seq'
  29
  30   if request.has_key('aflid'):
  31     AFL_Id = request['aflid']
  32     try:
  33       AFL = Affiliation.objects.get(id=AFL_Id).name
  34       AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
  35     except ObjectDoesNotExist:
  36       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
  37   else:
  38     AFL = 'ENCODE_Tier1'
  39     AFL_CNT = ''
  40     try:
  41       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
  42     except ObjectDoesNotExist:
  43       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
  44
  45   TFall = Library.objects.values('antibody').order_by('antibody').distinct()
  46   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
  47
  48   TFs = TFall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
  49   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
  50
  51   # Check Replicate numbers
  52   Reps = 1
  53   RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
  54   if len(RepRecs) > 0: Reps = RepRecs[0].replicate
  55
  56   ########
  57   str = ''
  58   str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self">Main Page</a></span>'
  59   ##str += '<span style="margin-right:20px">Max Replicates: '+MaxRep.replicate.__str__()+'</span>'
  60   str += '<span>Select another <b>'+EXP+'</b> Report:</span>  <select>'
  61   for af in Affiliation.objects.distinct():
  62     str += '<option value='+af.id.__str__()
  63     if AFL_Id == af.id.__str__():
  64       str += ' selected'
  65     str += ' onclick="window.location=\'/htsw_reports/report?aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
  66   str += '</select>'
  67
  68   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:#ff3300"> < 3 M</span></span>'
  69
  70   str += '<span style="margin-left:20px">'
  71   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>'
  72   str += '  | '
  73   str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
  74
  75   bgc = '#ffffff'
  76   pbgc = '#f7f7f7'
  77   str += '<br/><br/><table border=1>'
  78   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>'
  79   str += '<tr><th style="text-align:right">CELL LINE</th>'
  80   for H in CLLs:
  81     str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
  82     tbgc = bgc
  83     bgc = pbgc
  84     pbgc = tbgc
  85   str += '</tr><tr><th style="text-align:left">TF</th>'
  86   bgc = '#ffffff'
  87   pbgc = '#f7f7f7'
  88   for H in CLLs:
  89     for r in range(1,Reps+1):
  90       str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
  91     tbgc = bgc
  92     bgc = pbgc
  93     pbgc = tbgc
  94   str += '</tr>'
  95   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>'
  96   bgc = '#ffffff'
  97   pbgc = '#f7f7f7'
  98   for H in CLLs:
  99     for r in range(1,Reps+1):
 100       repReads = Library.objects.filter(experiment_type='INPUT_RXLCh',affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),replicate=r)
 101       str += "<td align=center style='background-color:"+bgc+"'>"
 102       if len(repReads) == 0:
 103         str += 'No Libraries'
 104       else:
 105         cnt = 0
 106         for R1 in repReads:
 107           rres = R1.aligned_m_reads()
 108           # Check data sanlty
 109           if rres[2] != 'OK':
 110             str += '<div style="border:solid red 2px">'+rres[2]
 111           else:
 112             cnt = rres[1]
 113             if cnt > 0:
 114               str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
 115               str += "%1.2f" % (cnt/1000000.0)+" M"
 116             else:  str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
 117           str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname
 118           if R1.libtags().find('Data submitted to DCC') != -1:
 119             str += "<div style='border:solid #666666 1px;background-color:#FFFFFF'>data submitted</div>"
 120           str += "</div>"
 121           str += "</div>"
 122       str += '</td>'
 123     tbgc = bgc
 124     bgc = pbgc
 125     pbgc = tbgc
 126   str += '</tr>'
 127
 128   for T in TFs:
 129     str += '<tr>'
 130     try:
 131       if T['antibody']:
 132         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>'
 133     except Antibody.DoesNotExist:
 134       str += '<td>n/a</td>'
 135
 136     bgc = '#ffffff'
 137     pbgc = '#f7f7f7'
 138     for H in CLLs:
 139       for r in range(1,Reps+1):
 140         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)
 141         str += "<td align=center style='background-color:"+bgc+"'>"
 142         if len(repReads) == 0:
 143           str += 'No Libraries'
 144         else:
 145           cnt = 0
 146           for R1 in repReads:
 147             rres = R1.aligned_m_reads()
 148             # Check data sanlty
 149             if rres[2] != 'OK':
 150               str += '<div style="border:solid red 2px">'+rres[2]
 151             else:
 152               cnt = rres[1]
 153               if cnt > 0:
 154                 str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%;margin:2px'>"
 155                 str += "%1.2f" % (cnt/1000000.0)+" M"
 156               else:  str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
 157             str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname
 158             if R1.libtags().find('Data submitted to DCC') != -1:
 159               str += "<div style='border:solid #666666 1px;background-color:#FFFFFF'>data submitted</div>"
 160             str += "</div>"
 161             str += "</div>"
 162         str += '</td>'
 163       tbgc = bgc
 164       bgc = pbgc
 165       pbgc = tbgc
 166     str += '</tr>'
 167   str += '</table>'
 168
 169   return render_to_response('htsw_reports/report.html',{'main': str})
 170
 171
 172 def report_RM(request): #for RNA-Seq and Methyl-Seq
 173   EXP = 'RNA-seq'
 174
 175   if request.has_key('exp'):
 176     EXP = request['exp'] # Methyl-seq
 177
 178   if request.has_key('aflid'):
 179     AFL_Id = request['aflid']
 180     try:
 181       AFL = Affiliation.objects.get(id=AFL_Id).name
 182       AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
 183     except ObjectDoesNotExist:
 184       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
 185   else:
 186     AFL = 'ENCODE_Tier1'
 187     AFL_CNT = ''
 188     try:
 189       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
 190     except ObjectDoesNotExist:
 191       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
 192
 193   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
 194   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
 195
 196   ########
 197   # Check Replicate numbers
 198   Reps = 1
 199   RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
 200   if len(RepRecs) > 0: Reps = RepRecs[0].replicate
 201
 202   str = ''
 203   str += '<span style="margin-right:20px"><a  target=_self href="/admin" target=_self">Main Page</a></span>'
 204   str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select>'
 205   for af in Affiliation.objects.distinct():
 206     str += '<option value='+af.id.__str__()
 207     if AFL_Id == af.id.__str__():
 208       str += ' selected'
 209     str += ' onclick="window.location=\'/htsw_reports/report_RM?exp='+EXP+'&aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
 210   str += '</select>'
 211
 212   if EXP == 'RNA-seq':
 213     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:#ff3300"> < 6 M</span></span>'
 214     str += '<span style="margin-left:20px">'
 215     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>'
 216     str += '  | '
 217     str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
 218   else:
 219     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:#ff3300"> < 3 M</span></span>'
 220     str += '<span style="margin-left:20px">'
 221     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>'
 222     str += '  | '
 223     str += '<a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
 224
 225   str += '<br/><br/><table border=1>'
 226   str += '<tr><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+'  <span style="font-size:140%">'+EXP+'</span></th></tr>'
 227   str += '<tr>'
 228   bgc = '#ffffff'
 229   pbgc = '#f7f7f7'
 230   for H in CLLs:
 231     str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
 232     tbgc = bgc
 233     bgc = pbgc
 234     pbgc = tbgc
 235   str += '</tr><tr>'
 236   bgc = '#ffffff'
 237   pbgc = '#f7f7f7'
 238   for H in CLLs:
 239     for r in range(1,Reps+1):
 240       str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
 241     tbgc = bgc
 242     bgc = pbgc
 243     pbgc = tbgc
 244   str += '</tr>'
 245
 246   str += '<tr>'
 247   bgc = '#ffffff'
 248   pbgc = '#f7f7f7'
 249   for H in CLLs:
 250     for r in range(1,Reps+1):
 251       repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'],replicate=r)
 252       str += "<td align=center valign=top style='background-color:"+bgc+"'>"
 253       if len(repReads) == 0:
 254         str += 'No Libraries'
 255       else:
 256         cnt = 0
 257         for R1 in repReads:
 258           rres = R1.aligned_m_reads()
 259           # Check data sanlty
 260           if rres[2] != 'OK':
 261             str += '<div style="border:solid red 2px">'+rres[2]
 262           else:
 263             cnt = rres[1]
 264             if cnt > 0:
 265               str += "<div style='background-color:"+getBgColor(cnt,EXP)+";border:solid #cccccc 1px;font-size:140%'>"
 266               str += "%1.2f" % (cnt/1000000.0)+" M"
 267             else:  str += "<div style='background-color:#ff3300;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
 268           str += "<div style='font-size:80%'><a title='View Record' target=_self href=/admin/fctracker/library/?q="+R1.library_id+">"+R1.library_id+"</a>, "+R1.condition.nickname+", "+R1.library_species.common_name+"</div>"
 269           str += "<div style='font-size:70%'>\""+R1.library_name+"\""
 270           if R1.libtags().find('Data submitted to DCC') != -1:
 271             str += "<div style='width:75%;border:solid #666666 1px;background-color:#FFFFFF'>data submitted</div>"
 272           str += "</div>"
 273           str += "</div>"
 274       str += '</td>'
 275     tbgc = bgc
 276     bgc = pbgc
 277     pbgc = tbgc
 278   str += '</tr>'
 279   str += '</table>'
 280
 281   return render_to_response('htsw_reports/report.html',{'main': str})
 282
 283 def getNotRanFCs(request):
 284   FCall = FlowCell.objects.order_by('-run_date').distinct()
 285   str = '<table><tr><th>FlowCell</th><th>Lanes</th><th>Creation Date</th></tr>'
 286   for f in FCall:
 287     try:
 288       t = DataRun.objects.get(fcid=f.id)
 289     except ObjectDoesNotExist:
 290       str += '<tr><td>'+f.flowcell_id+'</td><td>'+f.Lanes()+'</td><td>'+f.run_date.__str__()+'</td></tr>'
 291   str += "</table>"
 292   return render_to_response('htsw_reports/report.html',{'main':str})
 293
 294 def test_Libs(request):
 295   str = ''
 296   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>'
 297   allLibs = Library.objects.all()
 298   #allLibs = Library.objects.filter(antibody__isnull=False)
 299   for L in allLibs:
 300     str += '<tr>'
 301     str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
 302     str += '<td>'
 303     str += L.experiment_type+'_'
 304     if L.cell_line.cellline_name != 'Unknown':
 305       str += L.cell_line.cellline_name+'_'
 306
 307     try:
 308       if L.antibody is not None:
 309         str += L.antibody.nickname + '_'
 310     except Antibody.DoesNotExist:
 311       pass
 312
 313     str += 'Rep'+L.replicate.__str__()
 314     str += '</td></tr>'
 315
 316   str += '</table>'
 317   return HttpResponse(str)