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-rwxr-xr-xbin/genenetwork23
-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py57
-rw-r--r--wqflask/wqflask/templates/demo_correlation_page.html2
3 files changed, 47 insertions, 15 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 5f4e0f9a..917d6549 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -154,7 +154,8 @@ if [ ! -d $R_LIBS_SITE ] ; then
fi
# We may change this one:
-export PYTHONPATH=$PYTHON_GN_PATH:$GN2_BASE_DIR/wqflask:$PYTHONPATH
+# export PYTHONPATH=$PYTHON_GN_PATH:$GN2_BASE_DIR/wqflask:$PYTHONPATH
+PYTHONPATH=$PYTHON_GN_PATH:$GN2_BASE_DIR/wqflask:$HOME/genenetwork3:$PYTHONPATH
# Our UNIX TMPDIR defaults to /tmp - change this on a shared server
if [ -z $TMPDIR ]; then
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index b4480076..c1d6132b 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -1,11 +1,17 @@
"""module that calls the gn3 api's to do the correlation """
import json
import requests
+import time
from wqflask.correlation import correlation_functions
from base import data_set
from base.trait import create_trait
from base.trait import retrieve_sample_data
+# gn3 lib
+from gn3.computations.correlations import compute_all_sample_correlation
+from gn3.computations.correlations import benchmark_compute_all_sample
+from gn3.computations.correlations import map_shared_keys_to_values
+from gn3.computations.correlations import compute_all_tissue_correlation
GN3_CORRELATION_API = "http://127.0.0.1:8202/api/correlation"
@@ -30,7 +36,6 @@ def process_samples(start_vars, sample_names, excluded_samples=None):
def create_target_this_trait(start_vars):
"""this function creates the required trait and target dataset for correlation"""
-
print("creating the dataset and trait")
import time
@@ -52,11 +57,10 @@ def create_target_this_trait(start_vars):
target_dataset.get_trait_data(list(sample_data.keys()))
-
time_taken = time.time() - initial_time
- print(f"the time taken to create dataset is",time.time()-dataset_start_time)
+ print(f"the time taken to create dataset is", time.time()-dataset_start_time)
- print(f"the time taken to create dataset abnd trait is",time_taken)
+ print(f"the time taken to create dataset abnd trait is", time_taken)
return (this_dataset, this_trait, target_dataset, sample_data)
@@ -76,16 +80,34 @@ def compute_correlation(start_vars, method="pearson"):
corr_input_data = {}
if corr_type == "sample":
- corr_input_data = {
- "target_dataset": target_dataset.trait_data,
- "target_samplelist": target_dataset.samplelist,
- "trait_data": {
- "trait_sample_data": sample_data,
- "trait_id": start_vars["trait_id"]
- }
+ # corr_input_data = {
+ # "target_dataset": target_dataset.trait_data,
+ # "target_samplelist": target_dataset.samplelist,
+ # "trait_data": {
+ # "trait_sample_data": sample_data,
+ # "trait_id": start_vars["trait_id"]
+ # }
+ # }
+
+
+
+ this_trait_data = {
+ "trait_sample_data": sample_data,
+ "trait_id": start_vars["trait_id"]
}
- requests_url = f"{GN3_CORRELATION_API}/sample_x/{method}"
+ initial_time = time.time()
+ print("Calling sample correlation")
+ results = map_shared_keys_to_values(
+ target_dataset.samplelist, target_dataset.trait_data)
+ correlation_results = compute_all_sample_correlation(corr_method=method,
+ this_trait=this_trait_data,
+ target_dataset=results)
+
+ print("Time taken is>>>>",time.time()-initial_time)
+
+ # requests_url = f"{GN3_CORRELATION_API}/sample_x/{method}"
+ return correlation_results
elif corr_type == "tissue":
trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
@@ -96,8 +118,17 @@ def compute_correlation(start_vars, method="pearson"):
"primary_tissue": primary_tissue_data,
"target_tissues_dict": target_tissue_data
}
+ print("Calling tissue correlation")
+ initial_time = time.time()
+ correlation_results = compute_all_tissue_correlation(primary_tissue_dict=corr_input_data["primary_tissue"],
+ target_tissues_data=corr_input_data["target_tissues_dict"],
+ corr_method=method)
+
+ time_taken = time.time()
+ print("Time taken is ??????",time_taken-initial_time)
- requests_url = f"{GN3_CORRELATION_API}/tissue_corr/{method}"
+ # requests_url = f"{GN3_CORRELATION_API}/tissue_corr/{method}"
+ return correlation_results
elif corr_type == "lit":
(this_trait_geneid, geneid_dict, species) = do_lit_correlation(
diff --git a/wqflask/wqflask/templates/demo_correlation_page.html b/wqflask/wqflask/templates/demo_correlation_page.html
index 1900a0bd..d2979f9d 100644
--- a/wqflask/wqflask/templates/demo_correlation_page.html
+++ b/wqflask/wqflask/templates/demo_correlation_page.html
@@ -21,7 +21,7 @@
{% for corr_result in correlation_results %}
{% for key,value in corr_result.items()%}
<div class="container-content">
- <div><p>trait_name_here</p></div>
+ <div><p>{{key}}</p></div>
{%for o_key,o_value in value.items()%}
<div><p>{{o_value}}</p></div>
{%endfor%}