Add number of homologs to summary table

callbacks/general_util.py

@@ -57,6 +57,15 @@ def get_num_entries(table, column):
     return table[column].count()
 
 
+def count_non_empty_vals(array):
+    ctr = 0
+    for elem in array:
+        if elem != NULL_PLACEHOLDER:
+            ctr += 1
+
+    return ctr
+
+
 def purge_html_export_table(table):
     for row in table:
         for key in row.keys():

callbacks/lift_over/callbacks.py

@@ -2,7 +2,6 @@
 from dash.exceptions import PreventUpdate
 
 from .util import *
-from ..constants import Constants
 from ..general_util import *
 
 

callbacks/summary/callbacks.py

@@ -1,6 +1,7 @@
 from dash import Input, Output, State, html, ctx
 from dash.exceptions import PreventUpdate
 
+from .util import *
 from ..lift_over import util as lift_over_util
 from ..coexpression import util as coexpression_util
 
@@ -165,25 +166,30 @@ def display_summary_submitted_input(summary_is_submitted, coexpression_is_submit
     # Table-related
     # =================
 
-    # @app.callback(
-    #     Output('summary-results-table', 'data'),
-    #     Output('summary-results-table', 'columns'),
+    @app.callback(
+        Output('summary-results-table', 'data'),
+        Output('summary-results-table', 'columns'),
 
-    #     State('homepage-submitted-genomic-intervals', 'data'),
+        State('homepage-submitted-genomic-intervals', 'data'),
 
-    #     Input('summary-combined-genes', 'data'),
-    #     Input('summary-submitted-addl-genes', 'data'),
+        Input('summary-combined-genes', 'data'),
+        Input('summary-submitted-addl-genes', 'data'),
 
-    #     State('homepage-is-submitted', 'data'),
-    #     State('tfbs-is-submitted', 'data')
-    # )
-    # def display_enrichment_results(genomic_intervals, combined_genes, submitted_addl_genes,
-    #                                homepage_submitted, tfbs_is_submitted):
-    #     # if homepage_submitted and tfbs_is_submitted:
+        State('homepage-is-submitted', 'data'),
+        State('summary-is-submitted', 'data')
+    )
+    def display_summary_results(genomic_intervals, combined_genes, submitted_addl_genes,
+                                homepage_submitted, summary_is_submitted):
+        if homepage_submitted and summary_is_submitted:
+            summary_results_df = make_summary_table(
+                genomic_intervals, combined_genes)
 
-    #     #     return enrichment_results_df.to_dict('records'), columns, stats
+            columns = [{'id': x, 'name': x, 'presentation': 'markdown'}
+                       for x in summary_results_df.columns]
 
-    #     raise PreventUpdate
+            return summary_results_df.to_dict('records'), columns
+
+        raise PreventUpdate
 
     @app.callback(
         Output('summary-results-table', 'filter_query', allow_duplicate=True),

callbacks/summary/util.py

@@ -1,2 +1,34 @@
-def get_liftover_summary():
-    pass
+from ..lift_over.util import *
+from ..general_util import *
+
+from collections import defaultdict
+
+
+def get_liftover_summary(genomic_interval, implicated_genes):
+    all_genes = get_all_genes(other_ref_genomes.keys(),
+                              genomic_interval).values.tolist()
+
+    NB_IDX = 1
+    NB_PREFIX = 'LOC_Os'
+
+    gene_to_homologs_map = defaultdict(set)
+    for row in all_genes:
+        if row[NB_IDX].startswith(NB_PREFIX):
+            # Subtract 2 (i.e., subtract OGI)
+            for gene in row:
+                if gene != NULL_PLACEHOLDER:
+                    gene_to_homologs_map[row[NB_IDX]].add(gene)
+
+    print(gene_to_homologs_map)
+    gene_to_count = []
+    for gene, homologs in gene_to_homologs_map.items():
+        # Subtract 2 to remove OGI and Nipponbare
+        gene_to_count.append([gene, len(homologs) - 2])
+
+    gene_to_count_df = pd.DataFrame(
+        gene_to_count, columns=['Gene', '# Homologs'])
+    return gene_to_count_df
+
+
+def make_summary_table(genomic_interval, implicated_genes):
+    return get_liftover_summary(genomic_interval, implicated_genes)