htsworkflow/frontend/reports/reports.py

   1 from htsworkflow.frontend.experiments.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 'aflid' in request.GET:
  31     AFL_Id = request.GET['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 = str(Affiliation.objects.get(name=AFL).id)
  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   s = []
  58   s += ['<span style="margin-right:20px"><a target=_self href="/admin" target=_self">Main Page</a></span>']
  59   ##s += '<span style="margin-right:20px">Max Replicates: '+MaxRep.replicate.__str__()+'</span>'
  60   s += ['<span>Select another <b>'+EXP+'</b> Report:</span>  <select>']
  61   for af in Affiliation.objects.distinct():
  62     option = []
  63     option += ['<option value='+str(af.id)]
  64     if AFL_Id == str(af.id):
  65       option += [' selected']
  66     option += [' onclick="window.location=\'/reports/report?aflid='+af.id.__str__()+'\'; return false;">'+str(af.name)+' '+str(af.contact)+'</option>']
  67   s += option
  68   s += ['</select>']
  69
  70   s += ['<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>']
  71
  72   s += ['<span style="margin-left:20px">']
  73   s += ['<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>']
  74   s += ['  | ']
  75   s += ['<a target=_self href="/reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>']
  76
  77   bgc = '#ffffff'
  78   pbgc = '#f7f7f7'
  79   s += ['<br/><br/><table border=1 cellspacing="2">']
  80   s += ['<tr><th style="text-align:right">PROJECT</th><th colspan='+str(Reps*len(CLLs))+' style="text-align:center">'+AFL+' '+AFL_CNT+' <span style="font-size:140%">'+EXP+'</span></th></tr>']
  81   s += ['<tr><th style="text-align:right">CELL LINE</th>']
  82   for H in CLLs:
  83     s += ['<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>']
  84     tbgc = bgc
  85     bgc = pbgc
  86     pbgc = tbgc
  87   s += ['</tr><tr><th style="text-align:left">TF</th>']
  88   bgc = '#ffffff'
  89   pbgc = '#f7f7f7'
  90   for H in CLLs:
  91     for r in range(1,Reps+1):
  92       s += ['<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>']
  93     tbgc = bgc
  94     bgc = pbgc
  95     pbgc = tbgc
  96   s += ['</tr>']
  97   s += ['<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>']
  98   bgc = '#ffffff'
  99   pbgc = '#f7f7f7'
 100   for H in CLLs:
 101     for r in range(1,Reps+1):
 102       repReads = Library.objects.filter(experiment_type='INPUT_RXLCh',affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),replicate=r)
 103       s += ["<td align=center style='background-color:"+bgc+"'>"]
 104       if len(repReads) == 0:
 105         s += ['No Libraries']
 106       else:
 107         cnt = 0
 108         for R1 in repReads:
 109           rres = R1.aligned_m_reads()
 110           # Check data sanlty
 111           if rres[2] != 'OK':
 112             s += ['<div style="border:solid red 2px">'+rres[2]]
 113           else:
 114             cnt = rres[1]
 115             if cnt > 0:
 116               s += ["<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"]
 117               s += ["%1.2f" % (cnt/1000000.0)+" M"]
 118             else:
 119               s += ["<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"]
 120           s += ["<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"]
 121           s += ["</div>"]
 122       s += ['</td>']
 123     tbgc = bgc
 124     bgc = pbgc
 125     pbgc = tbgc
 126   s += ['</tr>' ]
 127
 128   for T in TFs:
 129     s += ['<tr>']
 130     try:
 131       if T['antibody']:
 132         s += ['<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       s += ['<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         s += ["<td align=center style='background-color:"+bgc+"'>"]
 142         if len(repReads) == 0:
 143           s += ['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               s += ['<div style="border:solid red 2px">'+rres[2]]
 151             else:
 152               cnt = rres[1]
 153               if cnt > 0:
 154                 s += ["<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"]
 155                 s += "%1.2f" % (cnt/1000000.0)+" M"
 156               else:
 157                 s += ["<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"]
 158             s += ["<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"]
 159             s += ["</div>"]
 160         s += ['</td>']
 161       tbgc = bgc
 162       bgc = pbgc
 163       pbgc = tbgc
 164     s += ['</tr>']
 165   s += ['</table>']
 166
 167   return render_to_response('reports/report.html',{'main': "\n".join(s)})
 168
 169
 170 def report_RM(request): #for RNA-Seq and Methyl-Seq
 171   EXP = 'RNA-seq'
 172
 173   if 'exp' in request.GET:
 174     EXP = request.GET['exp'] # Methyl-seq
 175
 176   if 'aflid' in request.GET:
 177     AFL_Id = request.GET['aflid']
 178     try:
 179       AFL = Affiliation.objects.get(id=AFL_Id).name
 180       AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
 181     except ObjectDoesNotExist:
 182       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
 183   else:
 184     AFL = 'ENCODE_Tier1'
 185     AFL_CNT = ''
 186     try:
 187       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
 188     except ObjectDoesNotExist:
 189       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
 190
 191   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
 192   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
 193
 194   ########
 195   # Check Replicate numbers
 196   Reps = 1
 197   RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
 198   if len(RepRecs) > 0: Reps = RepRecs[0].replicate
 199
 200   str = ''
 201   str += '<span style="margin-right:20px"><a  target=_self href="/admin" target=_self">Main Page</a></span>'
 202   str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select>'
 203   for af in Affiliation.objects.distinct():
 204     str += '<option value='+af.id.__str__()
 205     if AFL_Id == af.id.__str__():
 206       str += ' selected'
 207     str += ' onclick="window.location=\'/reports/report_RM?exp='+EXP+'&aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
 208   str += '</select>'
 209
 210   if EXP == 'RNA-seq':
 211     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>'
 212     str += '<span style="margin-left:20px">'
 213     str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/reports/report?exp=RNA-seq&aflid='+AFL_Id+'"><b>ChIP-Seq</b> Report</a>'
 214     str += '  | '
 215     str += '<a target=_self href="/reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
 216   else:
 217     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>'
 218     str += '<span style="margin-left:20px">'
 219     str += '<u>Switch to:</u> '+AFL+' '+AFL_CNT+' <a target=_self href="/reports/report?exp=RNA-seq&aflid='+AFL_Id+'"><b>ChIP-Seq</b> Report</a>'
 220     str += '  | '
 221     str += '<a target=_self href="/reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
 222
 223   str += '<br/><br/><table border=1 cellspacing="2">'
 224   str += '<tr><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+'  <span style="font-size:140%">'+EXP+'</span></th></tr>'
 225   str += '<tr>'
 226   bgc = '#ffffff'
 227   pbgc = '#f7f7f7'
 228   for H in CLLs:
 229     str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
 230     tbgc = bgc
 231     bgc = pbgc
 232     pbgc = tbgc
 233   str += '</tr><tr>'
 234   bgc = '#ffffff'
 235   pbgc = '#f7f7f7'
 236   for H in CLLs:
 237     for r in range(1,Reps+1):
 238       str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
 239     tbgc = bgc
 240     bgc = pbgc
 241     pbgc = tbgc
 242   str += '</tr>'
 243
 244   str += '<tr>'
 245   bgc = '#ffffff'
 246   pbgc = '#f7f7f7'
 247   for H in CLLs:
 248     for r in range(1,Reps+1):
 249       repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'],replicate=r)
 250       str += "<td align=center valign=top style='background-color:"+bgc+"'>"
 251       if len(repReads) == 0:
 252         str += 'No Libraries'
 253       else:
 254         cnt = 0
 255         for R1 in repReads:
 256           rres = R1.aligned_m_reads()
 257           # Check data sanlty
 258           if rres[2] != 'OK':
 259             str += '<div style="border:solid red 2px">'+rres[2]
 260           else:
 261             cnt = rres[1]
 262             if cnt > 0:
 263               str += "<div style='background-color:"+getBgColor(cnt,EXP)+";border:solid #cccccc 1px;font-size:140%'>"
 264               str += "%1.2f" % (cnt/1000000.0)+" M"
 265             else:  str += "<div style='background-color:#ff3300;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
 266           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>"
 267           str += "<div style='font-size:70%'>\""+R1.library_name+"\"</div"
 268           str += "</div>"
 269       str += '</td>'
 270     tbgc = bgc
 271     bgc = pbgc
 272     pbgc = tbgc
 273   str += '</tr>'
 274   str += '</table>'
 275
 276   return render_to_response('reports/report.html',{'main': str})
 277
 278 def getNotRanFCs(request):
 279   FCall = FlowCell.objects.order_by('-run_date').distinct()
 280   str = '<table><tr><th>FlowCell</th><th>Lanes</th><th>Creation Date</th></tr>'
 281   for f in FCall:
 282     try:
 283       t = DataRun.objects.get(fcid=f.id)
 284     except ObjectDoesNotExist:
 285       str += '<tr><td>'+f.flowcell_id+'</td><td>'+f.Lanes()+'</td><td>'+f.run_date.__str__()+'</td></tr>'
 286   str += "</table>"
 287   return render_to_response('reports/report.html',{'main':str})
 288
 289 def test_Libs(request):
 290   str = ''
 291   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>'
 292   allLibs = Library.objects.all()
 293   #allLibs = Library.objects.filter(antibody__isnull=False)
 294   for L in allLibs:
 295     str += '<tr>'
 296     str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
 297     str += '<td>'
 298     str += L.experiment_type+'_'
 299     if L.cell_line.cellline_name != 'Unknown':
 300       str += L.cell_line.cellline_name+'_'
 301
 302     try:
 303       if L.antibody is not None:
 304         str += L.antibody.nickname + '_'
 305     except Antibody.DoesNotExist:
 306       pass
 307
 308     str += 'Rep'+L.replicate.__str__()
 309     str += '</td></tr>'
 310
 311   str += '</table>'
 312   return HttpResponse(str)