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| author | zsloan | 2016-08-05 20:53:38 +0000 |
|---|---|---|
| committer | zsloan | 2016-08-05 20:53:38 +0000 |
| commit | ce160e61fffbc3370497a1adc299dad230411b72 (patch) | |
| tree | 1a99a3ba561df0690beaab70b2336c3384c7a57a /wqflask/wqflask | |
| parent | 08849a27af933340fc14decf8dfdd62e3d65b3b3 (diff) | |
| download | genenetwork2-ce160e61fffbc3370497a1adc299dad230411b72.tar.gz | |
Fixed issue that caused some interval mapping results to be wrong; the cause seems to be related to some strains being renamed in the genofiles
Added a message to the Add to Collection page warning users that anonymous collections will only be stored for 5 days
Updated genofiles
Diffstat (limited to 'wqflask/wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/add.html | 3 |
2 files changed, 11 insertions, 10 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index a8324442..89af856e 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -47,8 +47,6 @@ class MarkerRegression(object): helper_functions.get_species_dataset_trait(self, start_vars) - #tempdata = temp_data.TempData(temp_uuid) - self.temp_uuid = temp_uuid #needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py) self.json_data = {} @@ -59,11 +57,11 @@ class MarkerRegression(object): all_samples_ordered = self.dataset.group.all_samples_ordered() primary_sample_names = list(all_samples_ordered) - + for sample in self.dataset.group.samplelist: in_trait_data = False for item in self.this_trait.data: - if self.this_trait.data[item].name2 == sample: + if self.this_trait.data[item].name == sample: value = start_vars['value:' + self.this_trait.data[item].name] self.samples.append(self.this_trait.data[item].name) self.vals.append(value) @@ -280,7 +278,6 @@ class MarkerRegression(object): # print("json_data:", self.json_data) - self.js_data = dict( result_score_type = self.score_type, json_data = self.json_data, @@ -657,16 +654,15 @@ class MarkerRegression(object): genotype = genotype.addinterval() samples, values, variances, sample_aliases = self.this_trait.export_informative() - + trimmed_samples = [] trimmed_values = [] for i in range(0, len(samples)): - if self.this_trait.data[samples[i]].name2 in self.dataset.group.samplelist: - trimmed_samples.append(sample_aliases[i]) + #if self.this_trait.data[samples[i]].name2 in self.dataset.group.samplelist: + if self.this_trait.data[samples[i]].name in self.samples: + trimmed_samples.append(samples[i]) trimmed_values.append(values[i]) - #print("THE SAMPLES:", trimmed_samples) - if self.num_perm < 100: self.suggestive = 0 self.significant = 0 @@ -706,6 +702,8 @@ class MarkerRegression(object): control = control_geno, nboot = self.num_bootstrap) else: + # reaper_results = genotype.regression(strains = self.samples, + # trait = self.vals) reaper_results = genotype.regression(strains = trimmed_samples, trait = trimmed_values) diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html index f4a69423..c5598e84 100644 --- a/wqflask/wqflask/templates/collections/add.html +++ b/wqflask/wqflask/templates/collections/add.html @@ -23,6 +23,9 @@ <input type="text" name="new_collection" placeholder="Name of new collection..." data-trigger="change" data-minlength="5" data-maxlength="50"> <span class="help-block">Type the name of the new collection.</span> + {% if uc is not defined %} + <span class="help-block" style="color:red;">This collection will be saved to this computer for 5 days.</span> + {% endif %} <button type="submit" name="create_new" class="btn">Create and add traits</button> </fieldset> |