def main(request):
params = {}
params['queries'] = internal.ListQueries(request, {'projectID': [request.session['projectID']]})
params['attributes'] = internal.ListAttributes(request, {'projectID': [request.session['projectID']]})
queryname = request.GET.get('query') or None
inputdataset = request.GET.get('dataset') or None
method = request.GET.get('method') or None
category = request.GET.get('category') or None
attribute = request.GET.get('attribute') or None
mydata = {}
sa = {}
if queryname:
if not queryname or not inputdataset or not method or not category: return HttpResponse("required GET parameters: query, dataset, method, category" , content_type='text/plain')
dataset = internal.GetDataset(request, params={'queryname': [queryname], 'projectID': [request.session['projectID']], 'dataset': [inputdataset], 'category': [category], 'method': [method]})
attributes = internal.GetData(request, {'queryname': [queryname], 'projectID': [request.session['projectID']], 'attribute': [attribute,],})
attributes.pop(0)
for a in attributes: sa[a[0]] = a[1]
samples = list(set(dataset.values_list('sample', flat=True)))
for row in dataset:
if row.entity in mydata: mydata[row.entity][row.sample] = row.profile/100
else: mydata[row.entity] = {row.sample: row.profile/100}
inputfile = "/tmp/%d-%d-%s.txt" %(request.user.pk, int(time.time()), attribute.replace(' ', '_'))
formatfile = inputfile+".format"
resultfile = inputfile+".result"
with open(inputfile, 'w') as f:
f.write(attribute)
for s in samples:
if s in sa: f.write("\t"+str(sa[s]).lower())
else: f.write("\tNA")
f.write("\nsubject_id")
for s in samples: f.write("\t"+str(s))
for e in sorted(mydata):
f.write("\n"+e)
for s in samples:
if s in mydata[e]: f.write("\t"+str(mydata[e][s]))
else: f.write("\t0")
formatresp = myutils.runPython("lefse/format_input.py", inputfile, [formatfile, "-u2", "-o1000000"])
lefseresp = myutils.runPython("lefse/run_lefse.py", formatfile, [resultfile]).strip()
lefseresp = lefseresp.replace('\n', '<br />')
lefseresp = "<strong>Query:</strong> "+queryname+"<br><strong>Attribute:</strong> "+attribute+"<hr>"+lefseresp
#lefseresp = myutils.runCmd("python /home/orean/OREAN/scripts/misc/lefse/run_lefse.py "+ formatfile+" "+resultfile)
rows = ""
with open(resultfile, 'r') as f:
rows = f.read()
os.remove(inputfile)
os.remove(formatfile)
os.remove(resultfile)
return HttpResponse(json.dumps({'msg': lefseresp, 'data': rows}), content_type='application/json')
return render(request, "lefse.html", params)
def main(request):
params = {}
params['queries'] = internal.ListQueries(
request, {'projectID': [request.session['projectID']]})
params['attributes'] = internal.ListAttributes(
request, {'projectID': [request.session['projectID']]})
queryname = request.GET.get('query') or None
inputdataset = request.GET.get('dataset') or None
method = request.GET.get('method') or None
category = request.GET.get('category') or None
attribute = request.GET.get('attribute') or None
mydata = {}
sa = {}
if queryname:
if not queryname or not inputdataset or not method or not category:
return HttpResponse(
"required GET parameters: query, dataset, method, category",
content_type='text/plain')
dataset = internal.GetDataset(request,
params={
'queryname': [queryname],
'projectID':
[request.session['projectID']],
'dataset': [inputdataset],
'category': [category],
'method': [method]
})
attributes = internal.GetData(
request, {
'queryname': [queryname],
'projectID': [request.session['projectID']],
'attribute': [
attribute,
],
})
attributes.pop(0)
for a in attributes:
sa[a[0]] = a[1]
samples = list(set(dataset.values_list('sample', flat=True)))
for row in dataset:
if row.entity in mydata:
mydata[row.entity][row.sample] = row.profile / 100
else:
mydata[row.entity] = {row.sample: row.profile / 100}
inputfile = "/tmp/%d-%d-%s.txt" % (request.user.pk, int(
time.time()), attribute.replace(' ', '_'))
formatfile = inputfile + ".format"
resultfile = inputfile + ".result"
with open(inputfile, 'w') as f:
f.write(attribute)
for s in samples:
if s in sa: f.write("\t" + str(sa[s]).lower())
else: f.write("\tNA")
f.write("\nsubject_id")
for s in samples:
f.write("\t" + str(s))
for e in sorted(mydata):
f.write("\n" + e)
for s in samples:
if s in mydata[e]: f.write("\t" + str(mydata[e][s]))
else: f.write("\t0")
formatresp = myutils.runPython("lefse/format_input.py", inputfile,
[formatfile, "-u2", "-o1000000"])
lefseresp = myutils.runPython("lefse/run_lefse.py", formatfile,
[resultfile]).strip()
lefseresp = lefseresp.replace('\n', '<br />')
lefseresp = "<strong>Query:</strong> " + queryname + "<br><strong>Attribute:</strong> " + attribute + "<hr>" + lefseresp
#lefseresp = myutils.runCmd("python /home/orean/OREAN/scripts/misc/lefse/run_lefse.py "+ formatfile+" "+resultfile)
rows = ""
with open(resultfile, 'r') as f:
rows = f.read()
os.remove(inputfile)
os.remove(formatfile)
os.remove(resultfile)
return HttpResponse(json.dumps({
'msg': lefseresp,
'data': rows
}),
content_type='application/json')
return render(request, "lefse.html", params)
def main(request):
params = {}
params['queries'] = internal.ListQueries(request, {'projectID': [request.session['projectID']]})
params['attributes'] = internal.ListAttributes(request, {'projectID': [request.session['projectID']]})
querynamelist = 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
bothcount = 0
mydata = {}
sa = {}
if querynamelist:
if not len(querynamelist) == 2 or not inputdataset or not method or not category: return HttpResponse("required GET parameters: query, dataset, method, category, query2" , content_type='text/plain')
queryname, queryname2 = querynamelist
query1dataset = internal.GetDataset(request, params={'queryname': [queryname], 'projectID': [request.session['projectID']], 'dataset': [inputdataset], 'category': [category], 'method': [method]})
query2dataset = internal.GetDataset(request, params={'queryname': [queryname2], 'projectID': [request.session['projectID']], 'dataset': [inputdataset], 'category': [category], 'method': [method]})
#query1dataset = internal.GetDataset(request, params={'queryname': [queryname], 'projectID': [request.session['projectID']], 'dataset': [inputdataset], 'method': [method]})
#query2dataset = internal.GetDataset(request, params={'queryname': [queryname2], 'projectID': [request.session['projectID']], 'dataset': [inputdataset], 'method': [method]})
query1samples = internal.ListQueries(request, {'projectID': [request.session['projectID']], 'full': [True], 'queryname': [queryname]})[0]['results'].split(',')
query2samples = internal.ListQueries(request, {'projectID': [request.session['projectID']], 'full': [True], 'queryname': [queryname2]})[0]['results'].split(',')
totalsamples = list(set(query1samples+query2samples))
dataset = query1dataset | query2dataset
for s in totalsamples:
if s in query1samples and s in query2samples:
sa[s] = "Both"
bothcount+=1
elif s in query1samples and s not in query2samples:
sa[s] = queryname
elif s not in query1samples and s in query2samples:
sa[s] = queryname2
else:
return HttpResponse(json.dumps({'msg': "Could not determine how to group sample '%s'. Aborting LefSE analysis." % s, 'data': False}), content_type='application/json')
if bothcount == len(totalsamples): return HttpResponse(json.dumps({'msg': "Queries have the same sample composition. Cannot perform an analysis", 'data': False}), content_type='application/json')
samples = list(set(dataset.values_list('sample', flat=True)))
for row in dataset:
#if row.entity in mydata: mydata[row.entity][row.sample] = row.profile/100
#else: mydata[row.entity] = {row.sample: row.profile/100}
taxaName = row.entity
if row.taxatree is not None: taxaName = row.taxatree.full_tree
if taxaName in mydata: mydata[taxaName][row.sample] = row.profile/100
else: mydata[taxaName] = {row.sample: row.profile/100}
inputfile = "/tmp/%d-%d-lefse.txt" %(request.user.pk, int(time.time()))
formatfile = inputfile+".format"
resultfile = inputfile+".result"
with open(inputfile, 'w') as f:
f.write("QueryStatus")
for s in samples:
if s in sa: f.write("\t"+str(sa[s]).lower())
else: f.write("\tNA")
f.write("\nsubject_id")
for s in samples: f.write("\t"+str(s))
for e in sorted(mydata):
f.write("\n"+e)
for s in samples:
if s in mydata[e]: f.write("\t"+str(mydata[e][s]))
else: f.write("\t0")
formatresp = myutils.runPython("lefse/format_input.py", inputfile, [formatfile, "-u2", "-o1000000"])
lefseresp = myutils.runPython("lefse/run_lefse.py", formatfile, [resultfile]).strip()
lefseresp = lefseresp.replace('\n', '<br />')
lefseresp = "<strong>Query 1:</strong> "+queryname+"<br><strong>Query 2:</strong> "+queryname2+"<hr>"+lefseresp
#lefseresp = myutils.runCmd("python /home/orean/OREAN/scripts/misc/lefse/run_lefse.py "+ formatfile+" "+resultfile)
rows = ""
with open(resultfile, 'r') as f:
rows = f.read()
#os.remove(inputfile)
#os.remove(formatfile)
#os.remove(resultfile)
return HttpResponse(json.dumps({'msg': lefseresp, 'data': rows}), content_type='application/json')
return render(request, "lefse2.html", params)
