def tree(request, id, file, template='tree.html'):
"""Displays treenode results."""
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "data", "placementInfo")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
counts, headers = treeCsv(os.path.join(output, file, "treenodeCladeDist.tsv"))
if counts != None:
paginator = Paginator(counts, 50)
page = request.GET.get('page')
try:
counts = paginator.page(page)
except PageNotAnInteger:
counts = paginator.page(1)
except EmptyPage:
counts = paginator.page(paginator.num_pages)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
context = {
'counts': counts,
'headers': headers,
'id': id,
'file': file,
}
return render(request, template, context)
def perfect(request, id, template='subtypes.html'):
"""Displays subtypes results."""
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "data", "blastResults")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
counts, headers = csv2list(os.path.join(output, "PERFECT_subtypes_count.tsv"))
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("index", args=[sym_task.UID]))
context = {
'title': "Perfect Subtypes",
'counts': counts,
'headers': headers,
'id': id,
}
return render(request, template, context)
def perfect(request, id, template='subtypes.html'):
"""Displays subtypes results."""
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "data",
"blastResults")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
counts, headers = csv2list(
os.path.join(output, "PERFECT_subtypes_count.tsv"))
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("index", args=[sym_task.UID]))
context = {
'title': "Perfect Subtypes",
'counts': counts,
'headers': headers,
'id': id,
}
return render(request, template, context)
def chart(request, id, site):
"""Displays pie chart"""
detailed_counts = None
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "data",
"hmmer_parsedOutput")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
detailed_counts = searchTable(
os.path.join(output, 'DETAILED_counts.tsv'), site)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
return render_to_response(
'chart.html',
RequestContext(request, {
'id': id,
'site': site,
'detailed_counts': detailed_counts
}))
def unique(request, id, template='subtypes.html'):
"""Displays subtypes results."""
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "blastResults")
ready, redirect = taskReady(sym_task)
if ready:
counts, headers = csv2list(os.path.join(output, "UNIQUE_subtypes_count.tsv"))
#shortnew_counts, shortnew_headers = csv2list(os.path.join(output, "SHORTNEW_subtypes_count.tsv"))
#perfect_counts, perfect_headers = csv2list(os.path.join(output, "PERFECT_subtypes_count.tsv"))
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("index", args=[sym_task.UID]))
context = {
#'shortnew_counts': shortnew_counts,
#'shortnew_headers': shortnew_headers,
#'unique_counts': unique_counts,
#'unique_headers': unique_headers,
#'perfect_counts': perfect_counts,
#'perfect_headers': perfect_headers,
'counts': counts,
'headers': headers,
'title': "Unique Subtypes",
'id': id,
}
return render(request, template, context)
def clades(request, id, template='clades.html'):
"""Displays clade results."""
dirs = all_counts = detailed_counts = all_headers = detailed_headers = None
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "hmmer_parsedOutput")
ready, redirect = taskReady(sym_task)
if ready:
with open(os.path.join(output, "ALL_counts.tsv")) as tsv:
# order is maintained and we don't really reorder, so why use zip and dict?
all_headers = [ l for l in tsv.next().strip().split() ]
all_counts = [ row.strip().split() for row in tsv ]
with open(os.path.join(output, "DETAILED_counts.tsv")) as tsv:
# remove the sample
detailed_headers = tsv.next().strip().split()[1:]
detailed_counts = [ zip(detailed_headers, row.strip().split()[1:]) for row in tsv ]
paginator1 = Paginator(all_counts, 50)
paginator2 = Paginator(detailed_counts, 50)
page = request.GET.get('page')
try:
all_counts = paginator1.page(page)
detailed_counts = paginator2.page(page)
except PageNotAnInteger:
all_counts = paginator1.page(1)
detailed_counts = paginator2.page(1)
except EmptyPage:
all_counts_counts = paginator1.page(paginator.num_pages)
detailed_counts = paginator2.page(paginator.num_pages)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("index", args=[sym_task.UID]))
context = {
'id': id,
'title': "Clades",
'dirs': dirs,
'all_headers': all_headers,
'all_counts': all_counts,
'detailed_counts': detailed_counts,
#'detailed_headers': detailed_headers,
}
return render(request, template, context)
def multiplesResolved(request, id, file, template='multiples.html'):
"""Displays resolved multiples results."""
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
resolved = os.path.join(settings.SYMTYPER_HOME, str(id), "data",
"resolveMultiples", "correctedMultiplesHits",
"resolved")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
resolved_counts, resolved_headers, resolved_breakdown, resolved_subtypes = multiplesCsv(
os.path.join(resolved, file))
if resolved_counts != None and resolved_subtypes != None and resolved_breakdown != None:
paginator1 = Paginator(resolved_counts, 5)
paginator2 = Paginator(resolved_breakdown, 5)
paginator3 = Paginator(resolved_subtypes, 5)
page = request.GET.get('page')
try:
counts = paginator1.page(page)
breakdown = paginator2.page(page)
subtypes = paginator3.page(page)
except PageNotAnInteger:
counts = paginator1.page(1)
breakdown = paginator2.page(1)
subtypes = paginator3.page(1)
except EmptyPage:
counts = paginator1.page(paginator.num_pages)
breakdown = paginator2.page(paginator.num_pages)
subtypes = paginator3.page(paginator.num_pages)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
context = {
'file': file,
'counts': resolved_counts,
'headers': resolved_headers,
'breakdown': resolved_breakdown,
'subtypes': resolved_subtypes,
'id': id,
}
return render(request, template, context)
def dlEverything(request, id):
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
path = os.path.join(settings.SYMTYPER_HOME, str(id), "data")
return servZip(request, path)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
def dlEverything(request, id):
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
path = os.path.join(settings.SYMTYPER_HOME, str(id), "data")
return servZip(request, path)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
def multiplesResolved(request, id, file, template='multiples.html'):
"""Displays resolved multiples results."""
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
resolved = os.path.join(settings.SYMTYPER_HOME, str(id), "data", "resolveMultiples", "correctedMultiplesHits", "resolved")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
resolved_counts, resolved_headers, resolved_breakdown, resolved_subtypes = multiplesCsv(os.path.join(resolved, file))
if resolved_counts != None and resolved_subtypes != None and resolved_breakdown != None:
paginator1 = Paginator(resolved_counts, 5)
paginator2 = Paginator(resolved_breakdown, 5)
paginator3 = Paginator(resolved_subtypes, 5)
page = request.GET.get('page')
try:
counts = paginator1.page(page)
breakdown = paginator2.page(page)
subtypes = paginator3.page(page)
except PageNotAnInteger:
counts = paginator1.page(1)
breakdown = paginator2.page(1)
subtypes = paginator3.page(1)
except EmptyPage:
counts = paginator1.page(paginator.num_pages)
breakdown = paginator2.page(paginator.num_pages)
subtypes = paginator3.page(paginator.num_pages)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
context = {
'file': file,
'counts': resolved_counts,
'headers': resolved_headers,
'breakdown': resolved_breakdown,
'subtypes': resolved_subtypes,
'id': id,
}
return render(request, template, context)
def dlDetailed(request, id):
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
fPath = os.path.join(settings.SYMTYPER_HOME, str(id), "data", "hmmer_parsedOutput","DETAILED_counts.tsv")
fsize = os.stat(fPath).st_size
filename = "DETAILED_counts.tsv"
return servFile(request, ready, filename, fPath, fsize)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
def dlShortnew(request, id):
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
fPath = os.path.join(settings.SYMTYPER_HOME, str(id), "data", "blastResults","SHORTNEW_subtypes_count.tsv")
fsize = os.stat(fPath).st_size
filename = "SHORTNEW_subtypes__count.tsv"
return servFile(request, ready, filename, fPath, fsize)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
def dlBiom(request, id):
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task)
if ready:
fPath = os.path.join(settings.SYMTYPER_HOME, str(id), "breakdown.tsv")
fsize = os.stat(fPath).st_size
filename = "breakdown.tsv"
return servFile(request, ready, filename, fPath, fsize)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
def index(request, id, template='index.html'):
"""Displays index page."""
done = False
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task)
if ready:
done = True
elif redirect:
return redirect
else:
pass
#message = "pending..."
if done:
context = descriptiveStats(id)
params = yaml.load(sym_task.params)
parm = defaultdict(list)
version = params.pop('version_tag',1)
ordering = [p.title() for p in params.pop('order', [])]
if version == 1:
for k, v in params.iteritems():
section, label = k.replace('+',' ').split("_")
parm[section.title()].append( (label, v,))
for k in parm:
parm[k].sort(key = lambda x: x[0])
elif version == 2:
for section, v in params.iteritems():
k = section.title()
parm[k] = v.items()
parm[k].sort(key = lambda x: x[0])
context['done'] = done
context['id'] = id
context['params'] = dict(parm)
context['order'] = ordering
else:
context= {
'done': done,
'id': id
}
return render(request, template, context)
def dlDetailed(request, id):
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
fPath = os.path.join(settings.SYMTYPER_HOME, str(id), "data",
"hmmer_parsedOutput", "DETAILED_counts.tsv")
fsize = os.stat(fPath).st_size
filename = "DETAILED_counts.tsv"
return servFile(request, ready, filename, fPath, fsize)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
def dlShortnew(request, id):
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
fPath = os.path.join(settings.SYMTYPER_HOME, str(id), "data",
"blastResults", "SHORTNEW_subtypes_count.tsv")
fsize = os.stat(fPath).st_size
filename = "SHORTNEW_subtypes__count.tsv"
return servFile(request, ready, filename, fPath, fsize)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
def chart(request, id, site):
"""Displays pie chart"""
detailed_counts = None
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "data", "hmmer_parsedOutput")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
detailed_counts = searchTable(os.path.join(output, 'DETAILED_counts.tsv'),site)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
return render_to_response('chart.html', RequestContext(request, {'id': id, 'site': site, 'detailed_counts': detailed_counts}))
def dlMultiples(request, id):
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
ready, redirect = taskReady(sym_task)
if ready:
fPath = os.path.join(settings.SYMTYPER_HOME, str(id), "multiples.zip")
fsize = os.stat(fPath).st_size
filename = settings.SYMTYPER_ZIP_FMT%(str(id), "multiples")
return servFile(request, ready, filename, fPath, fsize)
path = os.path.join(settings.SYMTYPER_HOME, str(id), "resolveMultiples", "correctedMultiplesHits")
return servZip(request, path)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
def index(request, id, template='index.html'):
"""Displays index page."""
done = False
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
#output = os.path.join(settings.SYMTYPER_HOME, str(id), "data", "hmmer_parsedOutput")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
done = True
elif redirect:
return redirect
else:
pass
#message = "pending..."
context = {'done': done, 'id': id}
return render(request, template, context)
def index(request, id, template='index.html'):
"""Displays index page."""
done = False
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
#output = os.path.join(settings.SYMTYPER_HOME, str(id), "data", "hmmer_parsedOutput")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
done = True
elif redirect:
return redirect
else:
pass
#message = "pending..."
context = {
'done': done,
'id': id
}
return render(request, template, context)
def tree(request, id, file, template='tree.html'):
"""Displays treenode results."""
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "data",
"placementInfo")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
counts, headers = treeCsv(
os.path.join(output, file, "treenodeCladeDist.tsv"))
if counts != None:
paginator = Paginator(counts, 50)
page = request.GET.get('page')
try:
counts = paginator.page(page)
except PageNotAnInteger:
counts = paginator.page(1)
except EmptyPage:
counts = paginator.page(paginator.num_pages)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("status", args=[sym_task.UID]))
context = {
'counts': counts,
'headers': headers,
'id': id,
'file': file,
}
return render(request, template, context)
def clades(request, id, template='clades.html'):
"""Displays clade results."""
dirs = all_counts = detailed_counts = all_headers = detailed_headers = None
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id),
"data", "hmmer_parsedOutput")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
#dirs = [d for d in os.listdir(output)
#if os.path.isdir(os.path.join(output, d))]
with open(os.path.join(output, "ALL_counts.tsv")) as tsv:
all_counts = []
all = [line.strip().split() for line in tsv]
all_headers = all[0]
for row in all[1:]:
total = hit = no_hit = low = ambiguous = percentages = 0
site = row[0]
for column in row[1:]:
total += int(column)
if total != 0:
hit = round(float(row[1])/total * 100, 2)
no_hit = round(float(row[2])/total * 100, 2)
low = round(float(row[3])/total * 100, 2)
ambiguous = round(float(row[4])/total * 100, 2)
percentages = [site, hit, no_hit, low, ambiguous]
all_counts.append(dict(zip(all_headers, percentages)))
with open(os.path.join(output, "DETAILED_counts.tsv")) as tsv:
detailed_counts = []
all = [line.strip().split() for line in tsv]
detailed_headers = all[0][1:]
for row in all[1:]:
data = []
site = row[0]
for column in row[1:]:
data.append(column)
detailed_counts.append(dict(zip(detailed_headers, data)))
paginator1 = Paginator(all_counts, 50)
paginator2 = Paginator(detailed_counts, 50)
page = request.GET.get('page')
try:
all_counts = paginator1.page(page)
detailed_counts = paginator2.page(page)
except PageNotAnInteger:
all_counts = paginator1.page(1)
detailed_counts = paginator2.page(1)
except EmptyPage:
all_counts_counts = paginator1.page(paginator.num_pages)
detailed_counts = paginator2.page(paginator.num_pages)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("index", args=[sym_task.UID]))
context = {
'id': id,
'title': "Clades",
'dirs': dirs,
'all_headers': all_headers,
'all_counts': all_counts,
'detailed_counts': detailed_counts,
'detailed_headers': detailed_headers,
}
return render(request, template, context)
def clades(request, id, template='clades.html'):
"""Displays clade results."""
dirs = all_counts = detailed_counts = all_headers = detailed_headers = None
try:
sym_task = symTyperTask.objects.get(UID=id)
except ObjectDoesNotExist:
return HttpResponseRedirect(reverse("form"))
output = os.path.join(settings.SYMTYPER_HOME, str(id), "data",
"hmmer_parsedOutput")
ready, redirect = taskReady(sym_task.celeryUID)
if ready:
#dirs = [d for d in os.listdir(output)
#if os.path.isdir(os.path.join(output, d))]
with open(os.path.join(output, "ALL_counts.tsv")) as tsv:
all_counts = []
all = [line.strip().split() for line in tsv]
all_headers = all[0]
for row in all[1:]:
total = hit = no_hit = low = ambiguous = percentages = 0
site = row[0]
for column in row[1:]:
total += int(column)
if total != 0:
hit = round(float(row[1]) / total * 100, 2)
no_hit = round(float(row[2]) / total * 100, 2)
low = round(float(row[3]) / total * 100, 2)
ambiguous = round(float(row[4]) / total * 100, 2)
percentages = [site, hit, no_hit, low, ambiguous]
all_counts.append(dict(zip(all_headers, percentages)))
with open(os.path.join(output, "DETAILED_counts.tsv")) as tsv:
detailed_counts = []
all = [line.strip().split() for line in tsv]
detailed_headers = all[0][1:]
for row in all[1:]:
data = []
site = row[0]
for column in row[1:]:
data.append(column)
detailed_counts.append(dict(zip(detailed_headers, data)))
paginator1 = Paginator(all_counts, 50)
paginator2 = Paginator(detailed_counts, 50)
page = request.GET.get('page')
try:
all_counts = paginator1.page(page)
detailed_counts = paginator2.page(page)
except PageNotAnInteger:
all_counts = paginator1.page(1)
detailed_counts = paginator2.page(1)
except EmptyPage:
all_counts_counts = paginator1.page(paginator.num_pages)
detailed_counts = paginator2.page(paginator.num_pages)
elif redirect:
return redirect
else:
return HttpResponseRedirect(reverse("index", args=[sym_task.UID]))
context = {
'id': id,
'title': "Clades",
'dirs': dirs,
'all_headers': all_headers,
'all_counts': all_counts,
'detailed_counts': detailed_counts,
'detailed_headers': detailed_headers,
}
return render(request, template, context)
