From 413425b8ed3c69947b49ca366b210d69d2173805 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 13 May 2021 07:43:10 +0300
Subject: add dataset and trait-name in ui template
---
wqflask/wqflask/correlation/correlation_gn3_api.py | 103 +++++++++++++--------
.../wqflask/templates/test_correlation_page.html | 5 +-
wqflask/wqflask/views.py | 4 +-
3 files changed, 68 insertions(+), 44 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index 98d52591..e5638b5a 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -41,27 +41,33 @@ def process_samples(start_vars, sample_names, excluded_samples=None):
return sample_data
+def merge_correlation_results(correlation_results, target_correlation_results):
+
+ corr_dict = {}
+
+ for trait_dict in target_correlation_results:
+ for trait_name, values in trait_dict.items():
+
+ corr_dict[trait_name] = values
+ for trait_dict in correlation_results:
+ for trait_name, values in trait_dict.items():
+
+ if corr_dict.get(trait_name):
+
+ trait_dict[trait_name].update(corr_dict.get(trait_name))
+
+ return correlation_results
+
+
def sample_for_trait_lists(corr_results, target_dataset,
this_trait, this_dataset, start_vars):
"""interface function for correlation on top results"""
- sample_data = process_samples(
- start_vars, this_dataset.group.samplelist)
- target_dataset.get_trait_data(list(sample_data.keys()))
- # should filter target traits from here
- _corr_results = corr_results
-
- this_trait = retrieve_sample_data(this_trait, this_dataset)
-
- this_trait_data = {
- "trait_sample_data": sample_data,
- "trait_id": start_vars["trait_id"]
- }
- results = map_shared_keys_to_values(
- target_dataset.samplelist, target_dataset.trait_data)
+ (this_trait_data, target_dataset) = fetch_sample_data(
+ start_vars, this_trait, this_dataset, target_dataset)
correlation_results = compute_all_sample_correlation(corr_method="pearson",
this_trait=this_trait_data,
- target_dataset=results)
+ target_dataset=target_dataset)
return correlation_results
@@ -105,6 +111,23 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait):
return correlation_results
+def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
+
+ sample_data = process_samples(
+ start_vars, this_dataset.group.samplelist)
+ target_dataset.get_trait_data(list(sample_data.keys()))
+ this_trait = retrieve_sample_data(this_trait, this_dataset)
+ this_trait_data = {
+ "trait_sample_data": sample_data,
+ "trait_id": start_vars["trait_id"]
+ }
+
+ results = map_shared_keys_to_values(
+ target_dataset.samplelist, target_dataset.trait_data)
+
+ return (this_trait_data, results)
+
+
def compute_correlation(start_vars, method="pearson"):
"""compute correlation for to call gn3 api"""
# pylint: disable-msg=too-many-locals
@@ -119,31 +142,11 @@ def compute_correlation(start_vars, method="pearson"):
corr_input_data = {}
if corr_type == "sample":
-
- sample_data = process_samples(
- start_vars, this_dataset.group.samplelist)
- target_dataset.get_trait_data(list(sample_data.keys()))
- this_trait = retrieve_sample_data(this_trait, this_dataset)
- this_trait_data = {
- "trait_sample_data": sample_data,
- "trait_id": start_vars["trait_id"]
- }
- results = map_shared_keys_to_values(
- target_dataset.samplelist, target_dataset.trait_data)
+ (this_trait_data, target_dataset) = fetch_sample_data(
+ start_vars, this_trait, this_dataset, target_dataset)
correlation_results = compute_all_sample_correlation(corr_method=method,
this_trait=this_trait_data,
- target_dataset=results)
-
- # do tissue correaltion
-
- # code to be use later
-
- # tissue_result = tissue_for_trait_lists(
- # correlation_results, this_dataset, this_trait)
- # # lit spoils the party so slow
- # lit_result = lit_for_trait_list(
- # correlation_results, this_dataset, this_trait)
-
+ target_dataset=target_dataset)
elif corr_type == "tissue":
trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
@@ -172,7 +175,29 @@ def compute_correlation(start_vars, method="pearson"):
conn=conn, trait_lists=list(geneid_dict.items()),
species=species, gene_id=this_trait_geneid)
- return correlation_results[0:corr_return_results]
+ # correlation_results = correlation_results[0:corr_return_results]
+ # if corr_type != "tissue" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet":
+ # pass
+ # # tissue_result = tissue_for_trait_lists(
+ # # correlation_results, this_dataset, this_trait)
+
+ # # correlation_results = merge_correlation_results(
+ # # correlation_results, tissue_result)
+
+ # if corr_type != "lit" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet":
+ # pass
+ # # lit is very slow
+ # # lit_result = lit_for_trait_list(correlation_results, this_dataset, this_trait)
+ # # correlation_results = merge_correlation_results(correlation_results,lit_result)
+ # if corr_type != "sample":
+ # # do sample correlation
+ # pass
+ correlation_results = correlation_results[0:corr_return_results]
+ correlation_data = {"correlation_results": correlation_results,
+ "this_trait": this_trait.name,
+ "target_dataset": start_vars['corr_dataset']}
+
+ return correlation_data
def do_lit_correlation(this_trait, this_dataset):
diff --git a/wqflask/wqflask/templates/test_correlation_page.html b/wqflask/wqflask/templates/test_correlation_page.html
index 037e9735..186de4b7 100644
--- a/wqflask/wqflask/templates/test_correlation_page.html
+++ b/wqflask/wqflask/templates/test_correlation_page.html
@@ -42,7 +42,7 @@
{% block content %}
-
Correlation Results for Dataset_name against trait_name for the top all Results
+
Correlation Results for {{target_dataset}} against {{this_trait}} for the top all Results