added NCBoostv2

Author: vidboda

MobiDetailsApp/api.py

@@ -324,6 +324,8 @@ def variant(variant_id=None, caller='browser', api_key=None):
         },
         'nonCodingPredictions':{
             'mobideep': None,
+            'ncboostRaw': None,
+            'ncboostPhred': None,
             'promoterai': None,
             'remm': None,
         },
@@ -534,6 +536,7 @@ def variant(variant_id=None, caller='browser', api_key=None):
             'episignature': None,
             'mavedb': None,
             'morfeedb': None,
+            'ncboost': None, 
             'gpnmsa': None,
             'cactus241way': None,
             'remm': None,
@@ -1361,6 +1364,21 @@ def variant(variant_id=None, caller='browser', api_key=None):
                         else:
                             external_data['nonCodingPredictions']['promoterai'] = format(float(record[int(md_utilities.external_tools['PromoterAI']['raw_col'])]), '.2f')
                             internal_data['nonCodingPredictions']['promoteraiColor'] = md_utilities.get_preditor_single_threshold_color(abs(float(external_data['nonCodingPredictions']['promoterai'])), 'promoterai')
+
+
+
+                    # NCBoostv2
+                    if variant_features['prot_type'] == 'unknown':
+                        record = md_utilities.get_value_from_tabix_file('NCBoost', md_utilities.local_files['ncboost']['abs_path'], var, variant_features)
+                        if isinstance(record, str):
+                            internal_data['noMatch']['ncboost'] = "{0} {1}".format(record, md_utilities.external_tools['NCBoost']['version'])
+                        else:
+                            external_data['nonCodingPredictions']['ncboostRaw'] = format(float(record[int(md_utilities.external_tools['NCBoost']['raw_col'])]), '.4f')
+                            external_data['nonCodingPredictions']['ncboostPhred'] = format(float(record[int(md_utilities.external_tools['NCBoost']['phred_col'])]), '.4f')
+                            # internal_data['nonCodingPredictions']['promoteraiColor'] = md_utilities.get_preditor_single_threshold_color(abs(float(external_data['nonCodingPredictions']['ncboost'])), 'ncboost')
+
+
+
                     # GPN-MSA
                     record = md_utilities.get_value_from_tabix_file('GPN-MSA', md_utilities.local_files['gpnmsa']['abs_path'], var, variant_features)
                     if isinstance(record, str):

MobiDetailsApp/md_utilities.py

@@ -170,6 +170,9 @@ def get_resource_current_version(resource_dir, regexp, excluded_date=None):
 local_files['morfeedb_folder']['abs_path'] = '{0}{1}'.format(
     app_path, local_files['morfeedb_folder']['rel_path']
 )
+local_files['ncboost']['abs_path'] = '{0}{1}'.format(
+    app_path, local_files['ncboost']['rel_path']
+)
 oncokb_genes_version = get_resource_current_version(
     '{0}{1}'.format(app_path, local_files['oncokb_genes']['rel_path']),
     r'cancerGeneList_(\d+).tsv'
@@ -798,6 +801,7 @@ def get_value_from_tabix_file(text, tabix_file, var, variant_features, db=None):
             text == 'AbSplice' or \
             text == 'AlphaMissense' or \
             text == 'MorfeeDB'or \
+            text == 'NCBoost' or \
             text == 'GPN-MSA' :
         i -= 1
     if 'p_name' in variant_features and variant_features['p_name'] is not None:

MobiDetailsApp/sql/md_resources.yaml

@@ -163,6 +163,7 @@
   'ncbi_litvar_apiv2': 'https://www.ncbi.nlm.nih.gov/research/litvar2-api/variant/get/litvar%40'
   'ncbi_litvar_apiv2_sensor': 'https://www.ncbi.nlm.nih.gov/research/litvar2-api/sensor/'
   'ncbi_snp_api': 'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/'
+  'ncboost': 'https://github.com/RausellLab/NCBoost-2'
   'oncokb': 'https://www.oncokb.org/'
   'omim': 'http://omim.org/'
   'panelapp': 'https://panelapp.genomicsengland.co.uk/'
@@ -406,6 +407,11 @@
     'name': 'MMorfee scores'
     'description': 'bed files for MorfeeDB individual variants'
     'short_name': 'morfeedb_folder'
+  'ncboost':
+    'rel_path': '/static/resources/ncboost/ncboost_v2_hg38_20260202_light.tsv.gz'
+    'name': 'NCBoost v2 scores for 1.88 billion positions'
+    'description': 'Pre-computed NCBoost v2 scores'
+    'short_name': 'ncboost'
   'oncokb_genes':
     'rel_path': '/static/resources/oncokb/'
     'name': 'OncoKB cancer gene list'
@@ -785,6 +791,14 @@
     'paper': ' 27154141'
     'version': 'API'
     'short_name': 'mygene.info'
+  'NCBoost':
+    'firstauthor': 'Caron'
+    'year': '2026'
+    'paper': ''
+    'version': 'v20260202'
+    'short_name': 'ncboost'
+    'raw_col': '8'
+    'phred_col': '9'
   'OncoKBGenes':
     'firstauthor': 'Chakravarty'
     'year': '2017'

MobiDetailsApp/templates/md/variant.html

@@ -1520,7 +1520,7 @@
 				{{ content(internal_data.noMatch.morfeedb) }}
 			{% endif %}
 			{# {% if external_data.positions.proteinType == 'unknown' %} #}
-			{% if external_data.nonCodingPredictions.remm is not none or external_data.nonCodingPredictions.promoterai is not none or (external_data.positions.proteinType == 'unknown' and external_data.positions.DNAType == 'substitution')%}
+			{% if external_data.nonCodingPredictions.remm is not none or external_data.nonCodingPredictions.promoterai is not none or external_data.nonCodingPredictions.ncboostRaw is not none or (external_data.positions.proteinType == 'unknown' and external_data.positions.DNAType == 'substitution')%}
 			{{ section_subtitle('overall_nc_predictors', 'Overall non-coding predictors') }}
 			<div class="w3-responsive w3-container">
 				<table class="w3-table w3-centered display compact" style="width:90%" id="noncoding_table">
@@ -1532,7 +1532,7 @@
 						</tr>
 					</thead>
 					<tbody>
-						{% if internal_data.noMatch.remm is not none or external_data.nonCodingPredictions.remm is not none %}
+						{% if internal_data.noMatch.remm is none or external_data.nonCodingPredictions.remm is not none %}
 						<tr><!--ReMM-->
 							<td class="w3-left-align"><a href="{{ urls.remm }}" target="_blank" title="Visit ReMM" rel="noopener noreferrer">ReMM</a>:</td>
 							{% if internal_data.noMatch.remm is none %}
@@ -1543,7 +1543,7 @@
 							<td class="w3-left-align"><em class="w3-small">Threshold &gt; 0.924|0.961 for Likely Pathogenic and Pathogenic</em></td>
 						</tr>
 						{% endif %}
-						{% if internal_data.noMatch.promoterai is not none or external_data.nonCodingPredictions.promoterai is not none %}
+						{% if internal_data.noMatch.promoterai is none or external_data.nonCodingPredictions.promoterai is not none %}
 						<tr><!--PromoterAI-->
 							<td class="w3-left-align"><a href="{{ urls.promoterai }}" target="_blank" title="Visit PromoterAI" rel="noopener noreferrer">PromoterAI</a>:</td>
 							{% if internal_data.noMatch.promoterai is none %}
@@ -1554,6 +1554,17 @@
 							<td class="w3-left-align"><em class="w3-small">Prediction of expression altering promoter variants; Thresholds &le; -0.5 for under expression and &ge; 0.5 for over expression </em></td>
 						</tr>
 						{% endif %}
+						{% if internal_data.noMatch.ncboost is none or external_data.nonCodingPredictions.ncboostRaw is not none %}
+						<tr id="ncboost_tr">
+							<td class="w3-left-align"><a href="{{ urls.ncboost }}" target="_blank" title="Visit NCBoost v2" rel="noopener noreferrer">NCBoost v2</a>:</td>
+							{% if internal_data.noMatch.ncboost is none %}
+							<td class="w3-left-align" id="ncboost_score">{{ external_data.nonCodingPredictions.ncboostRaw }} ({{  external_data.nonCodingPredictions.ncboostPhred}}) </td>
+							{% else %}
+							<td class="w3-left-align">{{ internal_data.noMatch.ncboost }}</td>
+							{% endif %}
+							<td class="w3-left-align"><em class="w3-small">NCBoost raw score [0-1] (rank perc.). The rank percentile expresses the ranking of the variant among all variants lying in the same chromosome. The higher the most likely to have an impact</em></td>
+						</tr>
+						{% endif %}
 						<!--hidden tr for MobiDeep called by ajax-->
 						<tr id="mobideep_tr" style="display:none;">
 							<td class="w3-left-align"><a href="{{ urls.mobideep }}" target="_blank" title="Visit MobiDeep" rel="noopener noreferrer">MobiDeep</a>:</td>

tests/test_md_utilities.py

@@ -594,6 +594,7 @@ def test_acmg2lovd(app, acmg_class, lovd_class):
     ('gnomADv4 exome', var, '0.0015', 5, 'gnomad_4_exome', var_f),
     ('gnomADv4 exome', var_dup, '1.0000', 5, 'gnomad_4_exome', var_dup_f),
     ('Mistic', var, '0.876', 4, 'mistic', var_f),
+    ('NCBoost', var_5utr1, '0.1424310803413391', 8, 'ncboost', var_5utr1_f),
     ('dbscSNV', var_ss, '0.9999', 14, 'dbscsnv', var_ss_f),
     ('dbscSNV', var_ss, '0.928', 15, 'dbscsnv', var_ss_f),
     ('MorfeeDB', var_5utr1, 'uTIS', 10, 'morfeedb', var_5utr1_f),