diff options
| -rw-r--r-- | wqflask/wqflask/collect.py | 32 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 78 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 1 |
3 files changed, 15 insertions, 96 deletions
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 81d03d6c..bf465cdc 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -52,7 +52,7 @@ class AnonCollection(object): self.id = None self.created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') self.changed_timestamp = self.created_timestamp #ZS: will be updated when changes are made - + #ZS: Find id and set it if the collection doesn't already exist if Redis.get(self.key) == "None" or Redis.get(self.key) == None: Redis.set(self.key, None) #ZS: For some reason I get the error "Operation against a key holding the wrong kind of value" if I don't do this @@ -66,6 +66,7 @@ class AnonCollection(object): collection_exists = True self.id = collection['id'] break + if self.id == None: self.id = str(uuid.uuid4()) @@ -191,7 +192,19 @@ class UserCollection(object): # Probably have to change that return redirect(url_for('view_collection', uc_id=uc.id)) - +def process_traits(unprocessed_traits): + #print("unprocessed_traits are:", unprocessed_traits) + if isinstance(unprocessed_traits, basestring): + unprocessed_traits = unprocessed_traits.split(",") + traits = set() + for trait in unprocessed_traits: + #print("trait is:", trait) + data, _separator, hmac = trait.rpartition(':') + data = data.strip() + assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?" + traits.add (str(data)) + return traits + def report_change(len_before, len_now): new_length = len_now - len_before if new_length: @@ -224,7 +237,6 @@ def collections_add(): collections = collection_names, ) - @app.route("/collections/new") def collections_new(): params = request.args @@ -248,20 +260,6 @@ def collections_new(): else: CauseAnError - -def process_traits(unprocessed_traits): - #print("unprocessed_traits are:", unprocessed_traits) - if isinstance(unprocessed_traits, basestring): - unprocessed_traits = unprocessed_traits.split(",") - traits = set() - for trait in unprocessed_traits: - #print("trait is:", trait) - data, _separator, hmac = trait.rpartition(':') - data = data.strip() - assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?" - traits.add (str(data)) - return traits - def create_new(collection_name): params = request.args diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index f340e309..7ad5d25a 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -309,49 +309,6 @@ class MarkerRegression(object): perm_results = self.perm_output, ) - - def run_gemma(self): - """Generates p-values for each marker using GEMMA""" - - self.gen_pheno_txt_file() - - #os.chdir("/home/zas1024/gene/web/gemma") - - gemma_command = GEMMA_COMMAND + ' -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % ( - self.dataset.group.name, - self.dataset.group.name, - self.dataset.group.name) - #logger.debug("gemma_command:" + gemma_command) - - os.system(gemma_command) - - included_markers, p_values = self.parse_gemma_output() - - self.dataset.group.get_specified_markers(markers = included_markers) - self.dataset.group.markers.add_pvalues(p_values) - return self.dataset.group.markers.markers - - def parse_gemma_output(self): - included_markers = [] - p_values = [] - # Use a temporary file name here! - with open(webqtlConfig.GENERATED_TEXT_DIR+"/{}_output.assoc.txt".format(self.dataset.group.name)) as output_file: - for line in output_file: - if line.startswith("chr"): - continue - else: - included_markers.append(line.split("\t")[1]) - p_values.append(float(line.split("\t")[10])) - #p_values[line.split("\t")[1]] = float(line.split("\t")[10]) - #logger.debug("p_values: ", p_values) - return included_markers, p_values - - def gen_pheno_txt_file(self): - """Generates phenotype file for GEMMA""" - with open(webqtlConfig.GENERATED_TEXT_DIR+"{}.fam".format(self.dataset.group.name), "w") as outfile: - for i, sample in enumerate(self.samples): - outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(self.vals[i]) + "\n") - def run_rqtl_plink(self): # os.chdir("") never do this inside a webserver!! @@ -425,41 +382,6 @@ class MarkerRegression(object): output_file.close() - def gen_pheno_txt_file_rqtl(self, pheno_filename = ''): - ped_sample_list = self.get_samples_from_ped_file() - output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb") - header = 'FID\tIID\t%s\n' % self.this_trait.name - output_file.write(header) - - new_value_list = [] - - #if valueDict does not include some strain, value will be set to -9999 as missing value - for i, sample in enumerate(ped_sample_list): - try: - value = self.vals[i] - value = str(value).replace('value=','') - value = value.strip() - except: - value = -9999 - - new_value_list.append(value) - - - new_line = '' - for i, sample in enumerate(ped_sample_list): - j = i+1 - value = new_value_list[i] - new_line += '%s\t%s\t%s\n'%(sample, sample, value) - - if j%1000 == 0: - output_file.write(newLine) - new_line = '' - - if new_line: - output_file.write(new_line) - - output_file.close() - # get strain name from ped file in order def get_samples_from_ped_file(self): ped_file= open("{}/{}.ped".format(PLINK_PATH, self.dataset.group.name),"r") diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 598af0a6..1e831896 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -158,7 +158,6 @@ def verify_cookie(cookie): assert the_signature == actual_hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?" return the_uuid - def create_signed_cookie(): the_uuid = str(uuid.uuid4()) signature = actual_hmac_creation(the_uuid) |