--- /dev/null
+from htswfrontend.exp_track.models import *
+from django.http import HttpResponse
+from django.core.exceptions import ObjectDoesNotExist
+from django.shortcuts import render_to_response, get_object_or_404
+
+def getBgColor(reads_cnt,exp_type):
+ # 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
+ bgcolor = '#ff3300' # Red is the color for minimum read counts
+ rc_thr = [12000000,5000000,3000000] # Default for ChIP-Seq and Methyl-Seq
+ if exp_type == 'RNA-seq':
+ rc_thr = [20000000,10000000,6000000]
+
+ if reads_cnt > rc_thr[0]:
+ bgcolor = '#66ff66' # Green
+ else:
+ if reads_cnt > rc_thr[1]:
+ bgcolor ='#00ccff' # Blue
+ else:
+ if reads_cnt > rc_thr[2]:
+ bgcolor ='#ffcc33' # Orange
+ #tstr = '<div style="background-color:'+bgcolor+';color:black">'
+ #tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
+ #tstr += '</div>'
+
+ return bgcolor
+
+def report1(request):
+ EXP = 'ChIP-seq'
+
+ if request.has_key('aflid'):
+ AFL_Id = request['aflid']
+ try:
+ AFL = Affiliation.objects.get(id=AFL_Id).name
+ AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
+ except ObjectDoesNotExist:
+ return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
+ else:
+ AFL = 'ENCODE_Tier1'
+ AFL_CNT = ''
+ try:
+ AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
+ except ObjectDoesNotExist:
+ return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
+
+ TFall = Library.objects.values('antibody').order_by('antibody').distinct()
+ CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
+
+ TFs = TFall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+ CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+
+ # Check Replicate numbers
+ Reps = 1
+ RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
+ if len(RepRecs) > 0: Reps = RepRecs[0].replicate
+
+ ########
+ str = ''
+ str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self">Main Page</a></span>'
+ ##str += '<span style="margin-right:20px">Max Replicates: '+MaxRep.replicate.__str__()+'</span>'
+ str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select>'
+ for af in Affiliation.objects.distinct():
+ str += '<option value='+af.id.__str__()
+ if AFL_Id == af.id.__str__():
+ str += ' selected'
+ str += ' onclick="window.location=\'/htsw_reports/report?aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
+ str += '</select>'
+
+ 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>'
+
+ str += '<span style="margin-left:20px">'
+ 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>'
+ str += ' | '
+ str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
+
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ str += '<br/><br/><table border=1 cellspacing="2">'
+ 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>'
+ str += '<tr><th style="text-align:right">CELL LINE</th>'
+ for H in CLLs:
+ str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr><tr><th style="text-align:left">TF</th>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+ 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>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ repReads = Library.objects.filter(experiment_type='INPUT_RXLCh',affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'].__str__(),replicate=r)
+ str += "<td align=center style='background-color:"+bgc+"'>"
+ if len(repReads) == 0:
+ str += 'No Libraries'
+ else:
+ cnt = 0
+ for R1 in repReads:
+ cnt = R1.aligned_m_reads()[1]
+ if cnt > 0:
+ str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
+ str += "%1.2f" % (cnt/1000000.0)+" M"
+ else: str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
+ str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"
+ str += "</div>"
+ str += '</td>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+
+ for T in TFs:
+ str += '<tr>'
+ try:
+ if T['antibody']:
+ 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>'
+ except Antibody.DoesNotExist:
+ str += '<td>n/a</td>'
+
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ 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)
+ str += "<td align=center style='background-color:"+bgc+"'>"
+ if len(repReads) == 0:
+ str += 'No Libraries'
+ else:
+ cnt = 0
+ for R1 in repReads:
+ cnt = R1.aligned_m_reads()[1]
+ if cnt > 0:
+ str += "<div style='background-color:"+getBgColor(cnt,EXP)+";font-size:140%'>"
+ str += "%1.2f" % (cnt/1000000.0)+" M"
+ else: str += "<div style='background-color:#ff3300;width:100%;font-size:140%'>0 Reads"
+ str += "<div style='font-size:70%'>"+R1.library_id+", "+R1.condition.nickname+"</div>"
+ str += "</div>"
+ str += '</td>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+ str += '</table>'
+
+ return render_to_response('htsw_reports/report.html',{'main': str})
+
+
+def report_RM(request): #for RNA-Seq and Methyl-Seq
+ EXP = 'RNA-seq'
+
+ if request.has_key('exp'):
+ EXP = request['exp'] # Methyl-seq
+
+ if request.has_key('aflid'):
+ AFL_Id = request['aflid']
+ try:
+ AFL = Affiliation.objects.get(id=AFL_Id).name
+ AFL_CNT = Affiliation.objects.get(id=AFL_Id).contact
+ except ObjectDoesNotExist:
+ return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL_ID+"'")
+ else:
+ AFL = 'ENCODE_Tier1'
+ AFL_CNT = ''
+ try:
+ AFL_Id = Affiliation.objects.get(name=AFL,contact=AFL_CNT).id.__str__()
+ except ObjectDoesNotExist:
+ return HttpResponse("ERROR: Affiliation Record Not Found for: '"+AFL+"'")
+
+ CLLall = Library.objects.values('cell_line').order_by('cell_line').distinct()
+ CLLs = CLLall.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT)
+
+ ########
+ # Check Replicate numbers
+ Reps = 1
+ RepRecs = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT).order_by('-replicate')
+ if len(RepRecs) > 0: Reps = RepRecs[0].replicate
+
+ str = ''
+ str += '<span style="margin-right:20px"><a target=_self href="/admin" target=_self">Main Page</a></span>'
+ str += '<span>Select another <b>'+EXP+'</b> Report:</span> <select>'
+ for af in Affiliation.objects.distinct():
+ str += '<option value='+af.id.__str__()
+ if AFL_Id == af.id.__str__():
+ str += ' selected'
+ str += ' onclick="window.location=\'/htsw_reports/report_RM?exp='+EXP+'&aflid='+af.id.__str__()+'\'; return false;">'+af.name+' '+af.contact+'</option>'
+ str += '</select>'
+
+ if EXP == 'RNA-seq':
+ 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>'
+ str += '<span style="margin-left:20px">'
+ 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>'
+ str += ' | '
+ str += '<a target=_self href="/htsw_reports/report_RM?exp=Methyl-seq&aflid='+AFL_Id+'"><b>Methyl-Seq</b> Report</a>'
+ else:
+ 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>'
+ str += '<span style="margin-left:20px">'
+ 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>'
+ str += ' | '
+ str += '<a target=_self href="/htsw_reports/report_RM?exp=RNA-seq&aflid='+AFL_Id+'"><b>RNA-Seq</b> Report</a>'
+
+ str += '<br/><br/><table border=1 cellspacing="2">'
+ str += '<tr><th colspan='+(Reps*len(CLLs)).__str__()+' style="text-align:center">'+AFL+' '+AFL_CNT+' <span style="font-size:140%">'+EXP+'</span></th></tr>'
+ str += '<tr>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ str += '<th colspan='+Reps.__str__()+' style="text-align:center;background-color:'+bgc+'">'+Cellline.objects.get(id=H['cell_line']).cellline_name+'</th>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr><tr>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ str += '<th style="text-align:center;background-color:'+bgc+'">Rep. '+r.__str__()+'</th>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+
+ str += '<tr>'
+ bgc = '#ffffff'
+ pbgc = '#f7f7f7'
+ for H in CLLs:
+ for r in range(1,Reps+1):
+ repReads = Library.objects.filter(experiment_type=EXP,affiliations__name=AFL,affiliations__contact=AFL_CNT,cell_line=H['cell_line'],replicate=r)
+ str += "<td align=center valign=top style='background-color:"+bgc+"'>"
+ if len(repReads) == 0:
+ str += 'No Libraries'
+ else:
+ cnt = 0
+ for R1 in repReads:
+ cnt = R1.aligned_m_reads()[1]
+ if cnt > 0:
+ str += "<div style='background-color:"+getBgColor(cnt,EXP)+";border:solid #cccccc 1px;font-size:140%'>"
+ str += "%1.2f" % (cnt/1000000.0)+" M"
+ else: str += "<div style='background-color:#ff3300;border:solid #cccccc 1px;width:100%;font-size:140%'>0 Reads"
+ 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>"
+ str += "<div style='font-size:70%'>\""+R1.library_name+"\"</div"
+ str += "</div>"
+ str += '</td>'
+ tbgc = bgc
+ bgc = pbgc
+ pbgc = tbgc
+ str += '</tr>'
+ str += '</table>'
+
+ return render_to_response('htsw_reports/report.html',{'main': str})
+
+def getNotRanFCs(request):
+ FCall = FlowCell.objects.order_by('-run_date').distinct()
+ str = '<table><tr><th>FlowCell</th><th>Lanes</th><th>Creation Date</th></tr>'
+ for f in FCall:
+ try:
+ t = DataRun.objects.get(fcid=f.id)
+ except ObjectDoesNotExist:
+ str += '<tr><td>'+f.flowcell_id+'</td><td>'+f.Lanes()+'</td><td>'+f.run_date.__str__()+'</td></tr>'
+ str += "</table>"
+ return render_to_response('htsw_reports/report.html',{'main':str})
+
+def test_Libs(request):
+ str = ''
+ 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>'
+ allLibs = Library.objects.all()
+ #allLibs = Library.objects.filter(antibody__isnull=False)
+ for L in allLibs:
+ str += '<tr>'
+ str += '<td>'+L.library_id+'</td><td>'+L.library_name+'</td>'
+ str += '<td>'
+ str += L.experiment_type+'_'
+ if L.cell_line.cellline_name != 'Unknown':
+ str += L.cell_line.cellline_name+'_'
+
+ try:
+ if L.antibody is not None:
+ str += L.antibody.nickname + '_'
+ except Antibody.DoesNotExist:
+ pass
+
+ str += 'Rep'+L.replicate.__str__()
+ str += '</td></tr>'
+
+ str += '</table>'
+ return HttpResponse(str)
projects / htsworkflow.git / commitdiff