diff options
| -rw-r--r-- | wqflask/base/data_set.py | 3 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 40 | ||||
| -rw-r--r-- | wqflask/utility/helper_functions.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/collect.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 37 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_matrix.html | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/network_graph.html | 15 |
9 files changed, 95 insertions, 30 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index ca6621e9..beb2a8a2 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -277,7 +277,6 @@ class DatasetGroup(object): """ def __init__(self, dataset, name=None): """This sets self.group and self.group_id""" - #logger.debug("DATASET NAME2:", dataset.name) if name == None: self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) else: @@ -500,7 +499,7 @@ class DataSet(object): self.setup() if self.type == "Temp": #Need to supply group name as input if temp trait - self.group = DatasetGroup(self, group_name) # sets self.group and self.group_id and gets genotype + self.group = DatasetGroup(self, name=group_name) # sets self.group and self.group_id and gets genotype else: self.check_confidentiality() self.retrieve_other_names() diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 79aa196f..0689e950 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -6,6 +6,9 @@ import codecs from htmlgen import HTMLgen2 as HT +import redis +Redis = redis.StrictRedis() + from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset @@ -35,13 +38,15 @@ class GeneralTrait(object): def __init__(self, get_qtl_info=False, get_sample_info=True, **kw): # xor assertion assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; + self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. if kw.get('dataset_name'): - self.dataset = create_dataset(kw.get('dataset_name')) - #print(" in GeneralTrait created dataset:", self.dataset) + if kw.get('dataset_name') == "Temp": + temp_group = self.name.split("_")[2] + self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group) + else: + self.dataset = create_dataset(kw.get('dataset_name')) else: self.dataset = kw.get('dataset') - self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. - #print("THE NAME IS:", self.name) self.cellid = kw.get('cellid') self.identification = kw.get('identification', 'un-named trait') self.haveinfo = kw.get('haveinfo', False) @@ -73,8 +78,8 @@ class GeneralTrait(object): # So we could add a simple if statement to short-circuit this if necessary if self.dataset.type != "Temp": self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info) - if get_sample_info != False: - self = retrieve_sample_data(self, self.dataset) + if get_sample_info != False: + self = retrieve_sample_data(self, self.dataset) def export_informative(self, include_variance=0): """ @@ -154,18 +159,27 @@ def retrieve_sample_data(trait, dataset, samplelist=None): if samplelist == None: samplelist = [] - results = dataset.retrieve_sample_data(trait.name) + if dataset.type == "Temp": + results = Redis.get(trait.name).split() + else: + results = dataset.retrieve_sample_data(trait.name) # Todo: is this necessary? If not remove trait.data.clear() - all_samples_ordered = dataset.group.all_samples_ordered() - if results: - for item in results: - name, value, variance, num_cases, name2 = item - if not samplelist or (samplelist and name in samplelist): - trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) + if dataset.type == "Temp": + all_samples_ordered = dataset.group.all_samples_ordered() + for i, item in enumerate(results): + try: + trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item)) + except: + pass + else: + for item in results: + name, value, variance, num_cases, name2 = item + if not samplelist or (samplelist and name in samplelist): + trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) return trait @app.route("/trait/get_sample_data") diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 1c8dad10..6980af4e 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -45,7 +45,10 @@ def get_trait_db_obs(self, trait_db_list): data = data.strip() assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?" trait_name, dataset_name = data.split(":") - dataset_ob = data_set.create_dataset(dataset_name) + if dataset_name == "Temp": + dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2]) + else: + dataset_ob = data_set.create_dataset(dataset_name) trait_ob = GeneralTrait(dataset=dataset_ob, name=trait_name, cellid=None) diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index eb0e2726..6e1ac592 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -233,7 +233,10 @@ def collections_new(): collection_id = params['existing_collection'].split(":")[0] collection_name = params['existing_collection'].split(":")[1] if g.user_session.logged_in: - unprocessed_traits = Redis.get(params['hash']) + if "hash" in params: + unprocessed_traits = Redis.get(params['hash']) + else: + unprocessed_traits = params['traits'] traits = list(process_traits(unprocessed_traits)) g.user_session.add_traits_to_collection(collection_id, traits) return redirect(url_for('view_collection', uc_id=collection_id)) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index c15c3579..0c6b8a2b 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -93,7 +93,7 @@ class CorrelationResults(object): with Bench("Doing correlations"): if start_vars['dataset'] == "Temp": self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) - self.trait_id = "Temp" + self.trait_id = start_vars['trait_id'] self.this_trait = GeneralTrait(dataset=self.dataset, name=self.trait_id, cellid=None) diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 4bb4d65d..007e8e47 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -26,6 +26,7 @@ import sys import string import cPickle import os +import datetime import time import pp import math @@ -45,6 +46,9 @@ from pprint import pformat as pf from htmlgen import HTMLgen2 as HT import reaper +import redis +Redis = redis.StrictRedis() + from utility.THCell import THCell from utility.TDCell import TDCell from base.trait import GeneralTrait @@ -59,8 +63,10 @@ from MySQLdb import escape_string as escape from pprint import pformat as pf -from flask import Flask, g +from flask import Flask, g, url_for +import utility.logger +logger = utility.logger.getLogger(__name__ ) class CorrelationMatrix(object): @@ -111,6 +117,7 @@ class CorrelationMatrix(object): self.corr_results = [] self.pca_corr_results = [] self.trait_data_array = [] + self.shared_samples_list = self.all_sample_list for trait_db in self.trait_list: this_trait = trait_db[0] this_db = trait_db[1] @@ -138,6 +145,8 @@ class CorrelationMatrix(object): target_vals = [] for index, sample in enumerate(target_samples): if (sample in this_sample_data) and (sample in target_sample_data): + if sample not in self.shared_samples_list: + self.shared_samples_list.remove(sample) sample_value = this_sample_data[sample].value target_sample_value = target_sample_data[sample].value this_trait_vals.append(sample_value) @@ -174,6 +183,7 @@ class CorrelationMatrix(object): try: self.pca_works = "True" + self.pca_trait_ids = [] pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) self.loadings_array = self.process_loadings() except: @@ -201,9 +211,6 @@ class CorrelationMatrix(object): cellid=None) self.trait_list.append((trait_ob, dataset_ob)) - #print("trait_list:", self.trait_list) - - def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors): base = importr('base') stats = importr('stats') @@ -224,9 +231,27 @@ class CorrelationMatrix(object): pca_traits = [] for i, vector in enumerate(trait_array_vectors): if corr_eigen_value[i-1] < 100.0/len(self.trait_list): - pca_traits.append(vector*-1.0) + pca_traits.append((vector*-1.0).tolist()) + + this_group_name = self.trait_list[0][1].group.name + temp_dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = this_group_name) + temp_dataset.group.get_samplelist() + for i, pca_trait in enumerate(pca_traits): + trait_id = "PCA" + str(i+1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") + this_vals_string = "" + position = 0 + for sample in temp_dataset.group.all_samples_ordered(): + if sample in self.shared_samples_list: + this_vals_string += str(pca_trait[position]) + this_vals_string += " " + position += 1 + else: + this_vals_string += "x " + this_vals_string = this_vals_string[:-1] + + Redis.set(trait_id, this_vals_string) + self.pca_trait_ids.append(trait_id) - print("pca_traits:", pca_traits) return pca def process_loadings(self): diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 41d5c9d0..39e0d712 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -932,10 +932,13 @@ class DisplayMappingResults(object): if self.this_trait.symbol: identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.symbol) - elif self.this_trait.post_publication_abbreviation: - identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.post_publication_abbreviation) - elif self.this_trait.pre_publication_abbreviation: - identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.pre_publication_abbreviation) + elif self.dataset.type == "Publish": + if self.this_trait.post_publication_abbreviation: + identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.post_publication_abbreviation) + elif self.this_trait.pre_publication_abbreviation: + identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.pre_publication_abbreviation) + else: + identification += "Trait: %s" % (self.this_trait.name) else: identification += "Trait: %s" % (self.this_trait.name) identification += " with %s samples" % (self.n_samples) diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 8698b710..9c790780 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -60,6 +60,13 @@ {% if pca_works == "True" %} <br> <br> +<h2>PCA Traits</h2> +<ul> + {% for this_trait_id in pca_trait_ids %} + <li><a href="{{ url_for('show_trait_page', trait_id = pca_trait_ids[loop.index - 1], dataset = "Temp") }}">{{ pca_trait_ids[loop.index - 1] }}</a></li> + {% endfor %} +</ul> +<br> <h2>Factor Loadings Plot</h2> <div id="loadings_plot" style="margin-top: 20px; margin-bottom: 20px; width: 980px; border-style: solid; border-width: 1px;"></div> <h2>Factor Loadings Table</h2> diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html index 6bee11e7..4492dd3f 100644 --- a/wqflask/wqflask/templates/network_graph.html +++ b/wqflask/wqflask/templates/network_graph.html @@ -34,7 +34,11 @@ <select name="focus_select"> <option disabled selected value>Select Trait</option> {% for trait in traits %} + {% if trait.symbol == None %} + <option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.name }}</option> + {% else %} <option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.symbol }} ({{ trait.name }})</option> + {% endif %} {% endfor %} </select> </td> @@ -46,11 +50,18 @@ </tr> <tr> <td colspan="1"> + <div style="text-align: center;"> + <div style="float: left;"><font size="2"><b>-1</b></font></div> + <font size="2"><b>0</b></font> + <div style="float: right;"><font size="2"><b>1</b></font></div> + </div> + <!-- <font size="2"><b>-1 0 1</b></font><br> - <input type="range" id="neg_slide" min="-1" max="0" value="0" step="0.001" list="corr_range" style="display: inline; width: 45%"> - <input type="range" id="pos_slide" min="0" max="1" value="0" step="0.001" list="corr_range" style="display: inline; width: 45%"> + --> + <input type="range" id="neg_slide" min="-1" max="0" value="0" step="0.001" list="corr_range" style="display: inline; width: 49%"> + <input type="range" id="pos_slide" min="0" max="1" value="0" step="0.001" list="corr_range" style="display: inline; width: 49%"> </td> </tr> <tr> |