def get(self, request, slug, *args, **kwargs):
job_no = request.path_info.split("job")[-1]
results_folder = "%s/enrich/%s" % (get_path()[0], str(job_no))
par_name = "%s/parameter_file" % results_folder
if os.path.isfile(par_name):
parameters = get_parameter_dict(par_name)
tf = parameters['tf']
mode = parameters['mode']
centrimo_raw = "%s/%s/%s_centrimo.txt" % (results_folder, tf, tf)
t_head = get_table(centrimo_raw)[0]
t_body = get_table(centrimo_raw)[1]
job_no = results_folder.split("/")[-1]
display_img = '/static/files/enrich/%s/%s/' % (job_no, tf)
data = {'display_img': display_img, 'tf': tf, 'mode': mode,
't_body': t_body, 't_head': t_head}
return render(request, 'MATOM/assess_by_enrichment_results.html', context=data)
else:
return render(request, '404.html')
def get(self, request, slug, *args, **kwargs):
job_no = request.path_info.split("job")[-1]
print job_no
results_folder = "%s/score/%s" % (get_path()[0], str(job_no))
par_name = "%s/parameter_file" % results_folder
if os.path.isfile(par_name):
parameters = get_parameter_dict(par_name)
tf = parameters['tf']
mode = parameters['mode']
score_method = parameters['score']
data = self.plot_info(mode, tf, score_method, results_folder)
return render(request, 'MATOM/assess_by_score_results.html', context=data)
else:
return render(request, '404.html')
def post(self, request, *args, **kwargs):
# print "checking here"
form = self.form_class(request.POST)
if form.is_valid():
print "then here"
# print request.FILES['uploaded_motif']
query_string = request.POST.get('search')
#selected_project_id = query_string
tf_details_dict = {
}
entry_query = get_query(query_string, ['tf_name', 'alt_tf_name', ])
found_entries = TranscriptionFactor.objects.filter(entry_query)
if len(found_entries) == 1:
tf_class_id = found_entries[0].tf_id
Tf_exists = Matrix.objects.filter(tf_id=tf_class_id).exists()
chip_seq_exist = ChipSeq.objects.filter(tf_id=tf_class_id).exists()
pbm_exitst = Pbm.objects.filter(tf_id=tf_class_id).exists()
# TODO: Most of these should be in the models since they query DB. Keep business logic out
import re
if chip_seq_exist:
chipid = ChipSeq.objects.filter(tf_id=tf_class_id)[0].chip_id
chip_data = ChipData.objects.filter(chip_id=chipid).all()
chip_summary = []
for tf in chip_data:
a = str(tf.raw)
raw_file = re.split(r'([A-Z][a-z]*)', str(a))
cell_line = ''.join([raw_file[9], raw_file[10]])
lab = raw_file[7]
chip_summary.append([a, cell_line, lab])
else:
chip_summary = []
if pbm_exitst:
pbmid = Pbm.objects.filter(tf_id=tf_class_id)[0].pbm_id
pbm_data = PbmData.objects.filter(pbm_id=pbmid).all()
pbm_summary = []
for tf in pbm_data:
a = str(tf.source)
pbm_summary.append([a])
else:
pbm_summary = []
# Write a function, that uses these data to get the summary information.
#results_folder = '%s/MATOM/static/files/temp' % BASE_DIR
#results_folder = '%s/www/MARS/static/files/%s' % (home, method)
results_folder = "%stemp" % get_path()[0]
mkdir_p(results_folder)
if Tf_exists:
meme_out = '%s/temp.meme' % results_folder
with open(meme_out, "w") as out_file:
print "Lets get mmeme"
out_file.write(meme_head)
run_get_meme_id(tf_class_id, meme_out)
raw_out_file = '%s/temp_ic.txt' % results_folder
motif_ic.get_motif_summary_tfid(meme_out, raw_out_file, meme_path, results_folder)
t_head = get_table(raw_out_file)[0]
t_body = get_table(raw_out_file)[1]
else:
t_head = []
t_body = []
data = {'t_body': t_body, 't_head': t_head, 'chip_summary': chip_summary, 'pbm_summary': pbm_summary}
return render(request, template_name='MATOM/search_summary.html', context=data)
elif len(found_entries) == 0:
return redirect('/search/')
else:
for items in found_entries:
if found_entries is not None:
tf_details_dict[items.tf_id] = items.tf_name
#data = serializers.serialize('json', found_entries)
request.session['selected_project_id'] = tf_details_dict
# tf = request.POST.get('tf').lower()
# score_method = request.POST.get("score")
# mode = request.POST.get('mode')
# formats = request.POST.get('formats')
# pasted_motif = request.POST.get('test_motif')
# uploaded_motif = self.request.FILES.get('uploaded_motif')
# uploaded_chip = self.request.FILES.get('uploaded_chipseq')
# data = {
# 'found_entries': found_entries
# }
#form_html = render_to_string('search/search_results.html', context=data, request=request)
#return {'success': True, 'form_html': form_html}
return redirect('/search/select/')
ctx = {}
ctx.update(csrf(request))
form_html = render_crispy_form(form, context=ctx)
print "We got the form up and running"
return {'success': False, 'form_html': form_html}
def post(self, request, *args, **kwargs):
form = self.form_class(request.POST, request.FILES)
meme_error = None
if request.is_ajax():
print "We got here "
mode = request.POST.get('mode')
tf = request.POST.get('tf').lower()
pasted_motif = request.POST.get('test_motif')
uploaded_motif = self.request.FILES.get('uploaded_motif')
formats = request.POST.get('formats')
if formats:
if formats == 'upload' and uploaded_motif is None:
formats = False
print "Uploaded"
if formats == 'paste' and pasted_motif == "":
formats = False
print "pasted"
uploaded_chip = self.request.FILES.get('uploaded_chipseq')
tf_exists = Matrix.objects.filter(motif_name=tf).exists()
if tf != "":
if tf_exists or formats:
static_files = get_path(method="enrich")[0]
results_folder = static_files
motif_present_and_correct = self.handle_motifs(tf, pasted_motif, formats, results_folder, tf_exists)
if not motif_present_and_correct:
if tf_exists:
tf_class_id = MATOM.models.get_tf(tf)[0]
chipseq_exists = ChipSeq.objects.filter(tf_id=tf_class_id).exists()
chip_okay = self.process_chip(chipseq_exists, tf, results_folder)
if chip_okay:
chip_seq_list = chip_okay
results_folder_path = '%s/%s' % (results_folder, tf)
user_motif = "%s/%s/%s.meme" % (results_folder, tf, tf)
if mode == "CENTRIMO":
run_centrimo(tf, chip_seq_list, user_motif, results_folder_path, figure=True)
meme_file = "%s/%s/%s.meme" % (results_folder, tf, tf)
meme_out_file = "%s/%s/%s_ranked_by_%s.meme" % (results_folder, tf, tf, mode.lower())
centrimo_raw = "%s/%s/%s_centrimo_norm.txt" % (results_folder, tf, tf)
utils.extract_scored_meme(meme_file, meme_out_file, utils.get_dict(centrimo_raw))
centrimo_raw = "%s/%s/%s_centrimo.txt" % (results_folder, tf, tf)
t_head = get_table(centrimo_raw)[0]
t_body = get_table(centrimo_raw)[1]
job_no = results_folder.split("/")[-1]
display_img = '/static/files/enrich/%s/%s/%s_centrimo' % (job_no, tf, tf)
data = {'display_img': display_img, 'tf': tf, 'mode': mode,
't_body': t_body, 't_head': t_head}
form_html = render_to_string('MATOM/assess_by_enrichment_results.html',
context=data, request=request)
ctx = {}
ctx.update(csrf(request))
par_name = "%s/parameter_file" % results_folder
create_parameter_file(par_name, tf, mode)
return {'success': True, 'form_html': form_html, 'success_url': '/enrichment/job%s' % job_no}
else:
meme_error = 'NOT_AVAILABLE'
#context = {'message': error_message, 'form': form, 'tf': tf}
#return render(request, 'MATOM/assess_by_enrichment.html', context)
else:
meme_error = "BED_ERROR"
else:
meme_error = 'NO_CHIP'
else:
meme_error = motif_present_and_correct
else:
meme_error = "NO_TF"
else:
meme_error = "REQUIRED"
if os.path.exists(self.static_files):
import shutil
shutil.rmtree(self.static_files)
ctx = {}
ctx.update(csrf(request))
form_html = render_crispy_form(form, context=ctx)
return {'success': False, 'form_html': form_html, 'error_message': self.error_message, 'meme_error': meme_error}
def post(self, request, *args, **kwargs):
"""
"""
#static_files = self.static_files
if request.method == 'POST':
meme_error = None
print "pased here"
form = self.form_class(request.POST, request.FILES)
if request.is_ajax():
print "This is ajax"
mode = request.POST.get('mode')
tf = request.POST.get('tf')
formats = request.POST.get('formats')
pasted_motif = request.POST.get('test_motif')
uploaded_motif = self.request.FILES.get('uploaded_motif')
tf_exists = Matrix.objects.filter(motif_name=tf).exists()
print formats
if formats:
if formats == 'upload' and uploaded_motif is None:
formats = False
print "Uploaded"
if formats == 'paste' and pasted_motif == "":
formats = False
print "pasted"
# Ensure some form of motif has been entered by the user
# pasted_motif is not u"" or uploaded_motif
if tf != "":
if tf_exists or formats:
static_files = get_path(method="compare")[0]
results_folder = static_files
motif_present_and_correct = self.handle_motifs(tf, pasted_motif, formats, results_folder, tf_exists)
if not motif_present_and_correct:
if mode == "FISIM":
meme_file = "%s/%s/%s.meme" % (results_folder, tf, tf)
file_path = "%s/%s" % (results_folder, tf)
run_fisim(tf, meme_file, file_path, figure=True)
meme_out_file = "%s/%s/%s_ranked_by_fisim.meme" % (results_folder, tf, tf)
raw_file = "%s/%s/%s.fisim" % (results_folder, tf, tf)
# TODO: These are not being properly ranked, check it out
utils.extract_scored_meme(meme_file, meme_out_file, utils.get_dict(raw_file))
raw_out_file = "%s/%s/%s_ic.txt" % (results_folder, tf, tf)
motif_ic.get_motif_summary(meme_file, raw_file, tf, raw_out_file, meme_path, results_folder)
t_head = get_table(raw_out_file)[0]
t_body = get_table(raw_out_file)[1]
else:
meme_file = "%s/%s/%s.meme" % (results_folder, tf, tf)
file_path = "%s/%s" % (results_folder, tf)
run_tomtom(tf, meme_file, file_path, figure=True)
meme_out_file = "%s/%s/%s_ranked_by_tomtom.meme" % (results_folder, tf, tf)
raw_file = "%s/%s/%s.tomtom" % (results_folder, tf, tf)
needed_dict = utils.get_dict(raw_file)
utils.extract_scored_meme(meme_file, meme_out_file, needed_dict)
raw_out_file = "%s/%s/%s_ic.txt" % (results_folder, tf, tf)
motif_ic.get_motif_summary(meme_file, raw_file, tf, raw_out_file, meme_path, results_folder)
t_head = get_table(raw_out_file)[0]
t_body = get_table(raw_out_file)[1]
job_no = results_folder.split("/")[-1]
display_img = '/static/files/compare/%s/%s/%s_%s.png' % (job_no, tf, tf, mode.lower())
data = {'tf': tf, 'mode': mode, 'display_img': display_img, 't_body': t_body, 't_head': t_head}
form_html = render_to_string('MATOM/assess_by_comparison_results.html', context=data, request=request)
ctx = {}
ctx.update(csrf(request))
par_name = "%s/parameter_file" % results_folder
create_parameter_file(par_name, tf, mode)
return {'success': True, 'form_html': form_html, 'success_url': '/comparison/job%s' % job_no}
else:
meme_error = motif_present_and_correct
else:
meme_error = "NO_TF"
else:
meme_error = 'REQUIRED'
if os.path.exists(self.static_files):
import shutil
shutil.rmtree(self.static_files)
ctx = {}
ctx.update(csrf(request))
form_html = render_crispy_form(form, context=ctx)
return {'success': False, 'form_html': form_html, 'error_message': self.error_message,
'meme_error': meme_error}
def post(self, request, *args, **kwargs):
static_files = get_path("score")[0]
job_no = static_files.split("/")[-1]
meme_error = "ERROR"
# print "checking here"
form = self.form_class(request.POST, request.FILES)
if request.is_ajax():
print "then here"
# print request.FILES['uploaded_motif']
tf = request.POST.get('tf').lower()
score_method = request.POST.get("score")
mode = request.POST.get('mode')
formats = request.POST.get('formats')
pasted_motif = request.POST.get('test_motif')
uploaded_motif = self.request.FILES.get('uploaded_motif')
uploaded_chip = self.request.FILES.get('uploaded_chipseq')
data = request.POST.get('data')
if formats:
if formats == 'upload' and uploaded_motif is None:
formats = False
print "Uploaded"
if formats == 'paste' and pasted_motif == "":
formats = False
print "pasted"
tf_exists = Matrix.objects.filter(motif_name=tf).exists()
# pasted_motif is not u"" or uploaded_motif
#print job_no
if tf != "":
#static_files = get_path("score")[0]
#print static_files
if tf_exists or formats:
results_folder = static_files
print "TF exists or formats"
motif_present_and_correct = self.handle_motifs(tf, pasted_motif, formats, results_folder, tf_exists)
print motif_present_and_correct
if not motif_present_and_correct:
print "Motif is all good"
if tf_exists:
print "and there is a TF"
tf_class_id = MATOM.models.get_tf(tf)[0]
chipseq_exists = ChipSeq.objects.filter(tf_id=tf_class_id).exists()
if data == "ChIP-seq":
print "So we got here"
chip_okay = self.process_chip(chipseq_exists, tf, results_folder)
if not chipseq_exists and not chip_okay:
meme_error = "NO_CHIP"
else:
if chip_okay:
chip_seq_list = chip_okay
results_folder_path = '%s/%s' % (static_files, tf)
print results_folder_path
user_motif = "%s/%s/%s.meme" % (static_files, tf, tf)
files_path = '%s/%s/%s' % (results_folder, tf, tf)
if mode == "ASSESS":
Assess_by_score.run_all(tf, score_method, user_motif,
chip_seq_list, results_folder_path)
score_ext = Assess_by_score.score_extensions[score_method]
utils.extract_scored_meme(files_path + ".meme",
files_path + "_assess_ranked_by_" + score_ext + "_auc.meme",
utils.get_dict_assess(files_path + "." + score_ext, "AUC"))
# data = self.plot_info(mode, tf, score_method, results_folder)
# form_html = render_to_string('MATOM/assess_by_score_results.html',
# context=data, request=request)
par_name = "%s/parameter_file" % results_folder
create_parameter_file(par_name, tf, mode, score_method)
# 'form_html': form_html
return {'success': True, 'success_url': '/score/job%s' % job_no}
else:
run_gimme.run_gimme(tf, user_motif, chip_seq_list, results_folder_path, figure=True)
utils.extract_scored_meme(files_path + ".meme", files_path + "_gimme_ranked_by_" +
mode.lower() + "_auc.meme",
utils.get_dict_assess(files_path + "." +
mode.lower(), "AUC"))
par_name = "%s/parameter_file" % results_folder
create_parameter_file(par_name, tf, mode, score_method)
return {'success': True, 'success_url': '/score/job%s' % job_no}
#meme_error = "NOT_AVAILABLE"
else:
meme_error = "BED_ERROR"
else:
pbm_exists = Pbm.objects.filter(tf_id=tf_class_id).exists()
if pbm_exists:
print "We got to PBM"
pbm_list = glob.glob('%s/Data/PBM/%s/*' % (BASE_DIR, tf.capitalize()))
pbm_list_clean = []
for pbms in pbm_list:
if Assess_by_score_pbm.get_pbm_possitives(pbms) > 10:
pbm_list_clean.append(pbms)
if len(pbm_list_clean) > 0:
print "And pbm all good"
user_motif = "%s/%s/%s.meme" % (static_files, tf, tf)
results_folder_path = '%s/%s' % (static_files, tf)
Assess_by_score_pbm.run_all_pbm(tf, score_method, user_motif,
pbm_list_clean, results_folder_path)
files_path = '%s/%s/%s' % (results_folder, tf, tf)
score_ext = Assess_by_score.score_extensions[score_method]
utils.extract_scored_meme(files_path + ".meme",
files_path + "_assess_ranked_by_" + score_ext + "_auc.meme",
utils.get_dict_assess(files_path + "." + score_ext, "AUC"))
# data = self.plot_info(mode, tf, score_method, results_folder)
# form_html = render_to_string('MATOM/assess_by_score_results.html',
# context=data, request=request)
par_name = "%s/parameter_file" % results_folder
create_parameter_file(par_name, tf, mode, score_method)
# 'form_html': form_html,
return {'success': True, 'success_url': '/score/job%s' % job_no}
else:
meme_error = 'NO_PBM'
else:
meme_error = 'NO_PBM'
else:
meme_error = "NO_CHIP"
else:
meme_error = motif_present_and_correct
else:
meme_error = "NO_TF"
else:
meme_error = "REQUIRED"
#os.removedirs(self.static_files)
if os.path.exists(static_files):
import shutil
print "We had to delete"
shutil.rmtree(static_files)
ctx = {}
ctx.update(csrf(request))
form_html = render_crispy_form(form, context=ctx)
return {'success': False, 'form_html': form_html, 'error_message': self.error_message, 'meme_error': meme_error}
def post(self, request, *args, **kwargs):
# print "checking here"
form = self.form_class(request.POST)
print form.is_valid()
# TODO: Assuming for now that the form is valid
#if form.is_valid():
# print request.FILES['uploaded_motif']
tf_class_id = request.POST.get('tf_choices')
#Now lets validate available options
Tf_exists = Matrix.objects.filter(tf_id=tf_class_id).exists()
chip_seq_exist = ChipSeq.objects.filter(tf_id=tf_class_id).exists()
pbm_exitst = Pbm.objects.filter(tf_id=tf_class_id).exists()
# TODO: Most of these should be in the models since they query DB. Keep business logic out
import re
if chip_seq_exist:
chipid = ChipSeq.objects.filter(tf_id=tf_class_id)[0].chip_id
chip_data = ChipData.objects.filter(chip_id=chipid).all()
chip_summary = []
for tf in chip_data:
a = str(tf.raw)
raw_file = re.split(r'([A-Z][a-z]*)', str(a))
cell_line = ''.join([raw_file[9], raw_file[10]])
lab = raw_file[7]
chip_summary.append([a, cell_line, lab])
else:
chip_summary = []
if pbm_exitst:
pbmid = Pbm.objects.filter(tf_id=tf_class_id)[0].pbm_id
pbm_data = PbmData.objects.filter(pbm_id=pbmid).all()
pbm_summary = []
for tf in pbm_data:
a = str(tf.source)
pbm_summary.append([a])
else:
pbm_summary = []
# Write a function, that uses these data to get the summary information.
results_folder = "%s/temp" % get_path()[0]
print results_folder
if Tf_exists:
meme_out = '%stemp.meme' % results_folder
with open(meme_out, "w") as out_file:
print "Lets get mmeme"
out_file.write(meme_head)
run_get_meme_id(tf_class_id, meme_out)
raw_out_file = '%s/temp_ic.txt' % results_folder
motif_ic.get_motif_summary_tfid(meme_out, raw_out_file, meme_path, results_folder)
t_head = get_table(raw_out_file)[0]
t_body = get_table(raw_out_file)[1]
else:
t_head = []
t_body = []
data = {'t_body': t_body, 't_head': t_head, 'chip_summary': chip_summary, 'pbm_summary': pbm_summary}
return render(request, template_name='MATOM/search_summary.html', context=data)
