diff options
| -rw-r--r-- | misc/notes.txt | 3 | ||||
| -rwxr-xr-x[-rw-r--r--] | wqflask/wqflask/interval_mapping/interval_mapping.py | 70 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 44 |
3 files changed, 82 insertions, 35 deletions
diff --git a/misc/notes.txt b/misc/notes.txt index 91a0e67c..f6a2bb33 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -90,6 +90,9 @@ Reload web server: Run server: python runserver.py +Run sendmail.py +python send_mail.py + =========================================== UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index 5d660224..aca99cbe 100644..100755 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -89,26 +89,56 @@ class IntervalMapping(object): samples, values, variances = self.trait.export_informative() if self.control_locus: if self.weighted_regression: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, variance = variances, control = self.control_locus) else: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, control = self.control_locus) else: if self.weighted_regression: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, variance = variances) else: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values) - pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + + #if self.dataset.group.species == "human": + # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) + #else: + genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] + + no_val_samples = self.identify_empty_samples() + trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) + + genotype_matrix = np.array(trimmed_genotype_data).T + + #t_stats, p_values = lmm.run( + # pheno_vector, + # genotype_matrix, + # restricted_max_likelihood=True, + # refit=False, + # temp_data=tempdata + #) + + #self.dataset.group.markers.add_pvalues(p_values) + + #self.qtl_results = self.dataset.group.markers.markers + def gen_qtl_results_2(self, tempdata): + """Generates qtl results for plotting interval map""" + + self.dataset.group.get_markers() + self.dataset.read_genotype_file() + + pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + #if self.dataset.group.species == "human": # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) #else: @@ -131,36 +161,6 @@ class IntervalMapping(object): self.qtl_results = self.dataset.group.markers.markers - #def gen_qtl_results_2(self, tempdata): - # """Generates qtl results for plotting interval map""" - # - # self.dataset.group.get_markers() - # self.dataset.read_genotype_file() - # - # pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) - # - # #if self.dataset.group.species == "human": - # # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) - # #else: - # genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] - # - # no_val_samples = self.identify_empty_samples() - # trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) - # - # genotype_matrix = np.array(trimmed_genotype_data).T - # - # t_stats, p_values = lmm.run( - # pheno_vector, - # genotype_matrix, - # restricted_max_likelihood=True, - # refit=False, - # temp_data=tempdata - # ) - # - # self.dataset.group.markers.add_pvalues(p_values) - # - # self.qtl_results = self.dataset.group.markers.markers - def identify_empty_samples(self): no_val_samples = [] diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index deccf459..29f7f150 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -32,6 +32,7 @@ from base.data_set import create_datasets_list from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data from wqflask.marker_regression import marker_regression +from wqflask.interval_mapping import interval_mapping from wqflask.correlation import show_corr_results from utility import temp_data @@ -246,6 +247,49 @@ def marker_regression_page(): return rendered_template +@app.route("/interval_mapping", methods=('POST',)) +def interval_mapping_page(): + initial_start_vars = request.form + temp_uuid = initial_start_vars['temp_uuid'] + wanted = ( + 'trait_id', + 'dataset', + 'suggestive' + ) + + start_vars = {} + for key, value in initial_start_vars.iteritems(): + if key in wanted or key.startswith(('value:')): + start_vars[key] = value + + version = "v1" + key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True) + print("key is:", pf(key)) + with Bench("Loading cache"): + result = Redis.get(key) + + if result: + print("Cache hit!!!") + with Bench("Loading results"): + result = pickle.loads(result) + else: + print("Cache miss!!!") + template_vars = interval_mapping.IntervalMapping(start_vars, temp_uuid) + + template_vars.js_data = json.dumps(template_vars.js_data, + default=json_default_handler, + indent=" ") + + result = template_vars.__dict__ + + #causeerror + Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*60) + + with Bench("Rendering template"): + rendered_template = render_template("interval_mapping.html", **result) + + return rendered_template @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): |