diff options
| -rwxr-xr-x | bin/genenetwork2 | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 57 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/demo_correlation_page.html | 2 |
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%} |