From 0dd04c5ca0521f59f93b45663bdfd67c916a9f3c Mon Sep 17 00:00:00 2001 From: Arthur Centeno Date: Thu, 13 May 2021 08:05:30 +0000 Subject: Fix load_phenotypes to run with GN2 latest --- wqflask/wqflask/templates/tutorials.html | 1 + 1 file changed, 1 insertion(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html index ce5d0e3d..ed1b6f3a 100644 --- a/wqflask/wqflask/templates/tutorials.html +++ b/wqflask/wqflask/templates/tutorials.html @@ -10,6 +10,7 @@
  • Statistical and genetic functions, and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org
  • Webinar Series - Quantitative Genetics Tools for Mapping Trait Variation to Mechanisms, Therapeutics, and Interventions
    • +
  • TESTING

    • -- cgit v1.2.3 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

    Toggle Columns

    @@ -84,7 +84,6 @@ diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3c875163..4834ee63 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -972,8 +972,8 @@ def corr_compute_page(): @app.route("/test_corr_compute", methods=["POST"]) def test_corr_compute_page(): - correlation_results = compute_correlation(request.form) - return render_template("test_correlation_page.html", correlation_results=correlation_results) + correlation_data = compute_correlation(request.form) + return render_template("test_correlation_page.html", **correlation_data) @app.route("/corr_matrix", methods=('POST',)) def corr_matrix_page(): -- cgit v1.2.3 From 75b4e74dede48c59e07d8f15d2db4b5d6289c064 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 13 May 2021 08:25:42 +0300 Subject: integrate comute corr for top results in ui --- wqflask/wqflask/correlation/correlation_gn3_api.py | 68 ++++++++++++++++------ .../wqflask/templates/test_correlation_page.html | 5 +- 2 files changed, 54 insertions(+), 19 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index e5638b5a..dec84728 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -137,16 +137,19 @@ def compute_correlation(start_vars, method="pearson"): (this_dataset, this_trait, target_dataset, sample_data) = create_target_this_trait(start_vars) + target_dataset_type = target_dataset.type + this_dataset_type = this_dataset.type + method = start_vars['corr_sample_method'] corr_return_results = int(start_vars.get("corr_return_results", 100)) corr_input_data = {} if corr_type == "sample": - (this_trait_data, target_dataset) = fetch_sample_data( + (this_trait_data, target_dataset_data) = 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=target_dataset) + target_dataset=target_dataset_data) elif corr_type == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") @@ -175,31 +178,62 @@ def compute_correlation(start_vars, method="pearson"): conn=conn, trait_lists=list(geneid_dict.items()), species=species, gene_id=this_trait_geneid) - # 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 = correlation_results[0:corr_return_results] - # # correlation_results = merge_correlation_results( - # # correlation_results, tissue_result) + compute_all = True + + correlation_results = compute_corr_for_top_results(correlation_results, + this_trait, + this_dataset, + target_dataset, + corr_type) + + # if corr_type != "tissue" and this_dataset_type == "ProbeSet" and target_dataset_type == "ProbeSet": + + # tissue_result = tissue_for_trait_lists( + # correlation_results, this_dataset, this_trait) + + # if corr_type != "lit" and this_dataset_type == "ProbeSet" and target_dataset_type == "ProbeSet": + # lit_result = lit_for_trait_list( + # correlation_results, this_dataset, this_trait) - # 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']} + "target_dataset": start_vars['corr_dataset'], + "return_results": corr_return_results} return correlation_data +def compute_corr_for_top_results(correlation_results, + this_trait, + this_dataset, + target_dataset, + corr_type): + if corr_type != "tissue" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet": + + 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": + 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": + pass + + return correlation_results + + def do_lit_correlation(this_trait, this_dataset): """function for fetching lit inputs""" geneid_dict = this_dataset.retrieve_genes("GeneId") diff --git a/wqflask/wqflask/templates/test_correlation_page.html b/wqflask/wqflask/templates/test_correlation_page.html index 186de4b7..0809b65e 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 {{target_dataset}} against {{this_trait}} for the top all Results

    +

    Correlation Results for {{target_dataset}} against {{this_trait}} for the top {{return_results}} Results

    Toggle Columns

    @@ -137,7 +137,8 @@ console.log(correlationResults) { "targets":2, "render":(data,type,row)=>{ - let urlLink = "/show_trait?trait_id=1453207_at&dataset=HC_M2_0606_P" + // should use a dynamic dataset name + let urlLink = `/show_trait?trait_id=${data}&dataset=HC_M2_0606_P` let traitLink = `${data}` return traitLink }, -- cgit v1.2.3 From 01582f853420c6775bb891675fd2039a7fd5b3b8 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Thu, 13 May 2021 08:28:15 +0300 Subject: pep8 formatting & delete comments --- wqflask/wqflask/correlation/correlation_gn3_api.py | 24 +++++++--------------- 1 file changed, 7 insertions(+), 17 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index dec84728..46202ca3 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -180,25 +180,15 @@ def compute_correlation(start_vars, method="pearson"): correlation_results = correlation_results[0:corr_return_results] - compute_all = True + compute_all = True # later to be passed as argument - correlation_results = compute_corr_for_top_results(correlation_results, - this_trait, - this_dataset, - target_dataset, - corr_type) + if (compute_all): - # if corr_type != "tissue" and this_dataset_type == "ProbeSet" and target_dataset_type == "ProbeSet": - - # tissue_result = tissue_for_trait_lists( - # correlation_results, this_dataset, this_trait) - - # if corr_type != "lit" and this_dataset_type == "ProbeSet" and target_dataset_type == "ProbeSet": - # lit_result = lit_for_trait_list( - # correlation_results, this_dataset, this_trait) - - # if corr_type != "sample": - # pass + correlation_results = compute_corr_for_top_results(correlation_results, + this_trait, + this_dataset, + target_dataset, + corr_type) correlation_data = {"correlation_results": correlation_results, "this_trait": this_trait.name, -- cgit v1.2.3