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 request.GET.has_key('aflid'):
  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 = 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=\'/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="/reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
  72   str += '  | '
  73   str += '<a target=_self href="/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 cellspacing="2">'
  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+"</div>"
 118           str += "</div>"
 119       str += '</td>'
 120     tbgc = bgc
 121     bgc = pbgc
 122     pbgc = tbgc
 123   str += '</tr>'
 124
 125   for T in TFs:
 126     str += '<tr>'
 127     try:
 128       if T['antibody']:
 129         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>'
 130     except Antibody.DoesNotExist:
 131       str += '<td>n/a</td>'
 132
 133     bgc = '#ffffff'
 134     pbgc = '#f7f7f7'
 135     for H in CLLs:
 136       for r in range(1,Reps+1):
 137         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)
 138         str += "<td align=center style='background-color:"+bgc+"'>"
 139         if len(repReads) == 0:
 140           str += 'No Libraries'
 141         else:
 142           cnt = 0
 143           for R1 in repReads:
 144             rres = R1.aligned_m_reads()
 145             # Check data sanlty
 146             if rres[2] != 'OK':
 147               str += '<div style="border:solid red 2px">'+rres[2]
 148             else:
 149               cnt = rres[1]
 150               if cnt > 0:
 151                 str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
 152                 str += "%1.2f" % (cnt/1000000.0)+" M"
 153               else:  str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
 154             str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"
 155             str += "</div>"
 156         str += '</td>'
 157       tbgc = bgc
 158       bgc = pbgc
 159       pbgc = tbgc
 160     str += '</tr>'
 161   str += '</table>'
 162
 163   return render_to_response('reports/report.html',{'main': str})
 164
 165
 166 def report_RM(request): #for RNA-Seq and Methyl-Seq
 167   EXP = 'RNA-seq'
 168
 169   if request.GET.has_key('exp'):
 170     EXP = request.GET['exp'] # Methyl-seq
 171
 172   if request.GET.has_key('aflid'):
 173     AFL_Id = request.GET['aflid']
 174     try:
 175       AFL = Affiliation.objects.get(id=AFL_Id).name
 176       AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
 177     except ObjectDoesNotExist:
 178       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
 179   else:
 180     AFL = 'ENCODE_Tier1'
 181     AFL_CNT = ''
 182     try:
 183       AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
 184     except ObjectDoesNotExist:
 185       return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
 186
 187   CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
 188   CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
 189
 190   ########
 191   # Check Replicate numbers
 192   Reps = 1
 193   RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
 194   if len(RepRecs) > 0: Reps = RepRecs[0].replicate
 195
 196   str = ''
 197   str += '<span style="margin-right:20px"><a  target=_self href="/admin" target=_self">Main Page</a></span>'
 198   str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select>'
 199   for af in Affiliation.objects.distinct():
 200     str += '<option value='+af.id.__str__()
 201     if AFL_Id == af.id.__str__():
 202       str += ' selected'
 203     str += ' onclick="window.location=\'/reports/report_RM?exp='+EXP+'&aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
 204   str += '</select>'
 205
 206   if EXP == 'RNA-seq':
 207     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>'
 208     str += '<span style="margin-left:20px">'
 209     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>'
 210     str += '  | '
 211     str += '<a target=_self href="/reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
 212   else:
 213     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>'
 214     str += '<span style="margin-left:20px">'
 215     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>'
 216     str += '  | '
 217     str += '<a target=_self href="/reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
 218
 219   str += '<br/><br/><table border=1 cellspacing="2">'
 220   str += '<tr><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+'  <span style="font-size:140%">'+EXP+'</span></th></tr>'
 221   str += '<tr>'
 222   bgc = '#ffffff'
 223   pbgc = '#f7f7f7'
 224   for H in CLLs:
 225     str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
 226     tbgc = bgc
 227     bgc = pbgc
 228     pbgc = tbgc
 229   str += '</tr><tr>'
 230   bgc = '#ffffff'
 231   pbgc = '#f7f7f7'
 232   for H in CLLs:
 233     for r in range(1,Reps+1):
 234       str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
 235     tbgc = bgc
 236     bgc = pbgc
 237     pbgc = tbgc
 238   str += '</tr>'
 239
 240   str += '<tr>'
 241   bgc = '#ffffff'
 242   pbgc = '#f7f7f7'
 243   for H in CLLs:
 244     for r in range(1,Reps+1):
 245       repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'],replicate=r)
 246       str += "<td align=center valign=top style='background-color:"+bgc+"'>"
 247       if len(repReads) == 0:
 248         str += 'No Libraries'
 249       else:
 250         cnt = 0
 251         for R1 in repReads:
 252           rres = R1.aligned_m_reads()
 253           # Check data sanlty
 254           if rres[2] != 'OK':
 255             str += '<div style="border:solid red 2px">'+rres[2]
 256           else:
 257             cnt = rres[1]
 258             if cnt > 0:
 259               str += "<div style='background-color:"+getBgColor(cnt,EXP)+";border:solid #cccccc 1px;font-size:140%'>"
 260               str += "%1.2f" % (cnt/1000000.0)+" M"
 261             else:  str += "<div style='background-color:#ff3300;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
 262           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>"
 263           str += "<div style='font-size:70%'>\""+R1.library_name+"\"</div"
 264           str += "</div>"
 265       str += '</td>'
 266     tbgc = bgc
 267     bgc = pbgc
 268     pbgc = tbgc
 269   str += '</tr>'
 270   str += '</table>'
 271
 272   return render_to_response('reports/report.html',{'main': str})
 273
 274 def getNotRanFCs(request):
 275   FCall = FlowCell.objects.order_by('-run_date').distinct()
 276   str = '<table><tr><th>FlowCell</th><th>Lanes</th><th>Creation Date</th></tr>'
 277   for f in FCall:
 278     try:
 279       t = DataRun.objects.get(fcid=f.id)
 280     except ObjectDoesNotExist:
 281       str += '<tr><td>'+f.flowcell_id+'</td><td>'+f.Lanes()+'</td><td>'+f.run_date.__str__()+'</td></tr>'
 282   str += "</table>"
 283   return render_to_response('reports/report.html',{'main':str})
 284
 285 def test_Libs(request):
 286   str = ''
 287   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>'
 288   allLibs = Library.objects.all()
 289   #allLibs = Library.objects.filter(antibody__isnull=False)
 290   for L in allLibs:
 291     str += '<tr>'
 292     str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
 293     str += '<td>'
 294     str += L.experiment_type+'_'
 295     if L.cell_line.cellline_name != 'Unknown':
 296       str += L.cell_line.cellline_name+'_'
 297
 298     try:
 299       if L.antibody is not None:
 300         str += L.antibody.nickname + '_'
 301     except Antibody.DoesNotExist:
 302       pass
 303
 304     str += 'Rep'+L.replicate.__str__()
 305     str += '</td></tr>'
 306
 307   str += '</table>'
 308   return HttpResponse(str)