def main(request):
CUTOFF=20
params = {}
params['queries'] = internal.ListQueries(request, {'projectID': [request.session['projectID']]})
querynames = request.GET.getlist('query') or None
querynames = request.GET.getlist('query') or None
inputdataset = request.GET.get('dataset') or None
category = request.GET.get('category') or None
method = request.GET.get('method') or None
print querynames
if querynames:
if not querynames or not inputdataset or not method or not category: return render(request, 'alpha.html', params)
#entities = []
entities = myutils.topTaxa(request.session['projectID'], querynames, inputdataset, method, category, CUTOFF)
elementOfGlory = {en: {q:{} for q in querynames} for en in entities}
for query in querynames:
filename = "/tmp/%s-%d.txt" %(request.user.pk, int(time.time()))
datahash = {}
for ent in entities: datahash[ent] = []
longest_list = -1
print "Query:", query
dataset = internal.GetDataset(request, params={'queryname': [query], 'projectID': [request.session['projectID']], 'dataset': [inputdataset], 'category': [category], 'method': [method], 'entity': entities})
for d in dataset:
taxa = d.entity
datahash[taxa].append(d.profile)
if len(datahash[taxa]) > longest_list: longest_list = len(datahash[taxa])
with open(filename, 'a') as f:
for taxa in datahash:
f.write(str(taxa))
count = 0
for profile in datahash[taxa]:
count +=1
f.write(','+str(profile))
elementOfGlory[taxa][query]['n'] = str(count)
while count < longest_list:
f.write(','+str('0'))
count+=1
f.write('\n')
boxplot = myutils.runRscript('16sProfilesBoxplot.R', filename)
os.remove(filename)
tmp = boxplot.split('\n')
boxplot = []
for bp in tmp:
if bp == "": continue
tmp2 = bp.split(',')
tmp2 = [float(s) if isfloat(s) else s for s in tmp2]
if tmp2[0] in elementOfGlory: elementOfGlory[tmp2[0]][query]['stats'] = tmp2
else: elementOfGlory[tmp2[0]] = {query : {'stats': tmp2}}
finaldata = [ [], [], [], len(querynames) ]
i = 0
for en in entities:
for query in querynames:
bp = elementOfGlory[en][query]['stats']
bp.pop(0)
if len(bp[5:]): [finaldata[2].append([i,float(x)]) for x in bp[5:] if x != '']
finaldata[0].append(en+' ('+elementOfGlory[en][query].get('n', '?')+')')
finaldata[1].append(bp[:5])
i+=1
return HttpResponse(json.dumps(finaldata), content_type="application/json")
return render(request, '16sProfileBoxplot.html', params)
def alpha(request):
params = {}
params['queries'] = internal.ListQueries(request, {'projectID': [request.session['projectID']]})
querynames = request.GET.getlist('query') or None
inputdataset = request.GET.get('dataset') or None
method = request.GET.get('method') or None
category = request.GET.get('category') or None
if querynames:
if not querynames or not inputdataset or not method or not category: return render(request, 'alpha.html', params)
datapoints = []
outlierpoints = []
count = 0
for query in querynames:
entities = []
datahash = {}
dataset = internal.GetDataset(request, params={'queryname': [query], 'projectID': [request.session['projectID']], 'dataset': [inputdataset], 'category': [category], 'method': [method]})
for d in dataset:
if d.entity not in entities:
entities.append(d.entity)
if d.sample not in datahash: datahash[d.sample] = {}
datahash[d.sample][d.entity] = d.numreads
filename = "/tmp/%s-%d.txt" %(request.user.username, int(time.time()))
with open(filename, 'w') as f:
for taxa in entities: f.write(','+str(taxa))
f.write('\n')
for sample in datahash:
mycontent = sample
for taxa in entities:
mycontent+=','
if taxa in datahash[sample]: mycontent+=str(datahash[sample][taxa])
else: mycontent += str('0')
mycontent+='\n'
f.write(mycontent)
boxplot = myutils.runRscript('alphaDiversity.R', filename)
boxplot,outliers = boxplot.split('\n')[:2]
boxplot = boxplot.split(',')
outliers = outliers.split(',')
if len(boxplot): boxplot = [float(x) for x in boxplot]
if len(outliers): outliers = [[count,float(x)] for x in outliers if x != '']
os.remove(filename)
datapoints.append(boxplot)
outlierpoints.append(outliers)
count+=1
finaldata = [querynames, datapoints, outlierpoints]
return HttpResponse(json.dumps(finaldata), content_type="application/json")
return render(request, 'alpha.html', params)
def main(request):
params = {}
params['queries'] = internal.ListQueries(request, {'projectID': [request.session['projectID']]})
querynames = request.GET.getlist('query') or None
inputdataset = request.GET.get('dataset') or None
method = request.GET.get('method') or None
category = request.GET.get('category') or None
if querynames:
if not querynames or not inputdataset or not method or not category: return render(request, 'alpha.html', params)
entities = []
samples = []
datahash = {}
filename = "/tmp/%s-%d.txt" %(request.user.username, int(time.time()))
for query in querynames:
dataset = internal.GetDataset(request, params={'queryname': [query], 'projectID': [request.session['projectID']], 'dataset': [inputdataset], 'category': [category], 'method': [method]})
for d in dataset:
if d.entity not in entities:
entities.append(d.entity)
if d.sample not in samples:
samples.append(d.sample)
datahash[d.sample] = {'query' : [query]}
datahash[d.sample][d.entity] = d.profile
if query not in datahash[d.sample]['query']: datahash[d.sample]['query'].append(query)
with open(filename, 'w') as f:
f.write('Rank,Taxa,')
for sample in samples: f.write(str(sample)+',')
f.write('\n')
for entity in entities:
mycontent = category+','+entity+','
for sample in samples:
if entity in datahash[sample]: mycontent+=str(datahash[sample][entity])
else: mycontent += str('0')
mycontent+=','
mycontent+='\n'
f.write(mycontent)
pca = myutils.runRscript('pca.R', filename)
pca = pca.split('\n')
pca.pop(0)
pca.pop()
finaldata = [{'name' : querynames[0], 'color': '#ff0000', 'data': []}, {'name': querynames[1], 'color': '#0000ff', 'data': []}, {'name': 'Both', 'color': '#00ff00', 'data' : []}]
i = 0
for i in range(len(pca)):
row = pca[i]
if row.startswith('-----'): break
cols = row.split(',')
sample = cols[0]
if sample[0] == 'X' and sample not in datahash: sample = sample[1:]
xy = [float(cols[1]), float(cols[2])]
if len(datahash[sample]['query']) > 1: finaldata[2]['data'].append(xy)
elif querynames[0] in datahash[sample]['query']: finaldata[0]['data'].append(xy)
else: finaldata[1]['data'].append(xy)
i+=1
cutoff = i
variances = []
for i in range(cutoff, len(pca)):
row = pca[i]
if row.startswith('-----'): break
cols = row.split(',')
variances.append(cols)
i+=1
cutoff = i
finaldata.append(variances)
keytaxa = []
for i in range(cutoff, len(pca)):
row = pca[i]
cols = row.split(',')
keytaxa.append(cols)
finaldata.append(keytaxa)
#os.remove(filename)
return HttpResponse(json.dumps(finaldata), content_type="application/json")
return render(request, 'pca.html', params)
def main(request):
CUTOFF = 20
params = {}
params['queries'] = internal.ListQueries(
request, {'projectID': [request.session['projectID']]})
querynames = request.GET.getlist('query') or None
querynames = request.GET.getlist('query') or None
inputdataset = request.GET.get('dataset') or None
category = request.GET.get('category') or None
method = request.GET.get('method') or None
print querynames
if querynames:
if not querynames or not inputdataset or not method or not category:
return render(request, 'alpha.html', params)
#entities = []
entities = myutils.topTaxa(request.session['projectID'], querynames,
inputdataset, method, category, CUTOFF)
elementOfGlory = {en: {q: {} for q in querynames} for en in entities}
for query in querynames:
filename = "/tmp/%s-%d.txt" % (request.user.pk, int(time.time()))
datahash = {}
for ent in entities:
datahash[ent] = []
longest_list = -1
print "Query:", query
dataset = internal.GetDataset(request,
params={
'queryname': [query],
'projectID':
[request.session['projectID']],
'dataset': [inputdataset],
'category': [category],
'method': [method],
'entity':
entities
})
for d in dataset:
taxa = d.entity
datahash[taxa].append(d.profile)
if len(datahash[taxa]) > longest_list:
longest_list = len(datahash[taxa])
with open(filename, 'a') as f:
for taxa in datahash:
f.write(str(taxa))
count = 0
for profile in datahash[taxa]:
count += 1
f.write(',' + str(profile))
elementOfGlory[taxa][query]['n'] = str(count)
while count < longest_list:
f.write(',' + str('0'))
count += 1
f.write('\n')
boxplot = myutils.runRscript('16sProfilesBoxplot.R', filename)
os.remove(filename)
tmp = boxplot.split('\n')
boxplot = []
for bp in tmp:
if bp == "": continue
tmp2 = bp.split(',')
tmp2 = [float(s) if isfloat(s) else s for s in tmp2]
if tmp2[0] in elementOfGlory:
elementOfGlory[tmp2[0]][query]['stats'] = tmp2
else:
elementOfGlory[tmp2[0]] = {query: {'stats': tmp2}}
finaldata = [[], [], [], len(querynames)]
i = 0
for en in entities:
for query in querynames:
bp = elementOfGlory[en][query]['stats']
bp.pop(0)
if len(bp[5:]):
[
finaldata[2].append([i, float(x)]) for x in bp[5:]
if x != ''
]
finaldata[0].append(en + ' (' +
elementOfGlory[en][query].get('n', '?') +
')')
finaldata[1].append(bp[:5])
i += 1
return HttpResponse(json.dumps(finaldata),
content_type="application/json")
return render(request, '16sProfileBoxplot.html', params)
def alpha(request):
params = {}
params['queries'] = internal.ListQueries(
request, {'projectID': [request.session['projectID']]})
querynames = request.GET.getlist('query') or None
inputdataset = request.GET.get('dataset') or None
method = request.GET.get('method') or None
category = request.GET.get('category') or None
if querynames:
if not querynames or not inputdataset or not method or not category:
return render(request, 'alpha.html', params)
datapoints = []
outlierpoints = []
count = 0
for query in querynames:
entities = []
datahash = {}
dataset = internal.GetDataset(request,
params={
'queryname': [query],
'projectID':
[request.session['projectID']],
'dataset': [inputdataset],
'category': [category],
'method': [method]
})
for d in dataset:
if d.entity not in entities:
entities.append(d.entity)
if d.sample not in datahash: datahash[d.sample] = {}
datahash[d.sample][d.entity] = d.numreads
filename = "/tmp/%s-%d.txt" % (request.user.username,
int(time.time()))
with open(filename, 'w') as f:
for taxa in entities:
f.write(',' + str(taxa))
f.write('\n')
for sample in datahash:
mycontent = sample
for taxa in entities:
mycontent += ','
if taxa in datahash[sample]:
mycontent += str(datahash[sample][taxa])
else:
mycontent += str('0')
mycontent += '\n'
f.write(mycontent)
boxplot = myutils.runRscript('alphaDiversity.R', filename)
boxplot, outliers = boxplot.split('\n')[:2]
boxplot = boxplot.split(',')
outliers = outliers.split(',')
if len(boxplot): boxplot = [float(x) for x in boxplot]
if len(outliers):
outliers = [[count, float(x)] for x in outliers if x != '']
os.remove(filename)
datapoints.append(boxplot)
outlierpoints.append(outliers)
count += 1
finaldata = [querynames, datapoints, outlierpoints]
return HttpResponse(json.dumps(finaldata),
content_type="application/json")
return render(request, 'alpha.html', params)