scout-browser 4.89.1__py3-none-any.whl → 4.90__py3-none-any.whl

scout/server/blueprints/variants/templates/variants/components.html

@@ -1,4 +1,6 @@
-{% macro variant_gene_symbols_cell(variant) %}
+{% from "variant/gene_disease_relations.html" import inheritance_badge %}
+
+{% macro variant_gene_symbols_cell(variant, inherit_palette) %}
   <div class="d-flex justify-content-between align-items-center">
     <div>
       {% if variant.hgnc_symbols|length >= 5 %}
@@ -16,7 +18,30 @@
           {% if variant.hgnc_symbols %}
             <span class="badge bg-secondary mr-3 text-white">{{ variant.hgnc_symbols|length }}</span>
           {% endif %}
-          <span class="text-body">{{variant.hgnc_symbols|sort|join(", ")}}</span>
+          {% for gene in variant.genes %}
+            <a data-bs-toggle="tooltip" data-bs-html="true" title="
+            <div>
+              <div>
+                <strong>{{ gene.hgnc_symbol }}</strong>: {{ gene.description }}
+              </div>
+              {% if gene.inheritance %}
+                <div>
+                  <strong>Models</strong>: {{ gene.inheritance|join(',') }}
+                </div>
+              {% endif %}
+              {% if gene.phenotypes %}
+                <div><strong>OMIM disease</strong>
+                {% for disease in gene.phenotypes %}
+                  <div>
+                      {{ disease.description }}
+                  </div>
+                {% endfor %}
+                </div>
+              {% endif %}
+            </div>"
+              href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}">{{ gene.hgnc_symbol or gene.hgnc_id }}
+              {% for model in gene.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}</a>
+          {% endfor %}
         </div>
       {% endif %}
     </div>
@@ -38,8 +63,8 @@
       <th id="frame_status" style="width:8%" title="Frame status of the fusion">Frame Status</th>
       <th id="transcripts" style="width:8%" title="Transcript ID">Transcript ID</th>
       <th id="exons" style="width:4%" title="Exon Number">Exon Number</th>
-      <th id="brealpoints" style="width:4%" title="Breakpoints">Breakpoints</th>
-      <th id="oriantation" style="width:4%" title="Orientation">Orientation</th>
+      <th id="breakpoints" style="width:4%" title="Breakpoints">Breakpoints</th>
+      <th id="orientation" style="width:4%" title="Orientation">Orientation</th>
     </tr>
   </thead>
 {% endmacro %}
@@ -100,10 +125,20 @@
 
 {% macro variant_funct_anno_cell(variant) %}
   <div class="d-flex justify-content-between align-items-center">
-    <div>
-      {% if variant.category == "fusion" %}
-        {{ variant.frame_status|lower if variant.frame_status else "-" }}
+    <div data-bs-toggle="tooltip" data-bs-html="true" title="<div class='text-start'>
+      {% if variant.functional_annotations|length >= 5 %}
+        Regional annotations<br>
+        {% if variant.missing_data %}[first 30 genes]{% endif %}
+        {% for annotation in variant.region_annotations|sort %}
+          {{ annotation }}<br>
+        {% endfor %}
       {% else %}
+        {{ variant.region_annotations|sort|join(', ') }}
+      {% endif %}
+    </div>">
+    {% if variant.category == "fusion" %}
+      {{ variant.frame_status|lower if variant.frame_status else "-" }}
+    {% else %}
         {% if variant.functional_annotations|length >= 5 %}
           <a class="mr-3" data-bs-toggle="collapse" href="#_functanno_{{variant._id}}" role="button" aria-expanded="false" aria-controls="_{{variant._id}}">{% if variant.missing_data %}[first 30 genes]{% else %}[...]{% endif %}</a>
           <div class="collapse" id="_functanno_{{variant._id}}">
@@ -123,26 +158,8 @@
   </div>
 {% endmacro %}
 
-{% macro variant_region_anno_cell(variant) %}
-  <div class="d-flex justify-content-between align-items-center">
-    <div>
-      {% if variant.functional_annotations|length >= 5 %}
-        <a class="mr-3" data-bs-toggle="collapse" href="#_regionanno_{{variant._id}}" role="button" aria-expanded="false" aria-controls="_{{variant._id}}">{% if variant.missing_data %}[first 30 genes]{% else %}[...]{% endif %}</a>
-        <div class="collapse" id="_regionanno_{{variant._id}}">
-          {% for annotation in variant.region_annotations|sort %}
-            {{ annotation }}<br>
-          {% endfor %}
-        </div>
-      {% else %}
-        <div>
-          {{ variant.region_annotations|sort|join(", ") }}
-        </div>
-      {% endif %}
-    </div>
-  </div>
-{% endmacro %}
 
-{% macro gene_cell(variant) %}
+{% macro gene_cell(variant, inherit_palette) %}
   <div class="align-items-center">
     {% if variant.category == "cancer" or variant.category == "sv_cancer" %}
       <a data-bs-toggle="tooltip" data-bs-html="true" title="
@@ -191,7 +208,9 @@
           </a>
       {% endif %}
     {% else %}
+      {% set panel_count = variant.case_panels|rejectattr('removed')|list|count %}
       {% for gene in variant.genes %}
+        <div>
         <a data-bs-toggle="tooltip" data-bs-html="true" title="
         <div>
           <div>
@@ -213,12 +232,8 @@
           {% endif %}
         </div>"
           href="{{ url_for('genes.gene', hgnc_id=gene.hgnc_id) }}">{{ gene.hgnc_symbol or gene.hgnc_id }}
-        </a>
-      {% endfor %}
-
-
-      {% set panel_count = variant.case_panels|rejectattr('removed')|list|count %}
-      {% if panel_count > 0 %}
+        {% for model in gene.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}</a>
+        {% if panel_count > 0 %}
           <a
             class="badge bg-secondary text-white"
             data-bs-toggle="popover"
@@ -229,7 +244,10 @@
               {% endfor %}"
             title="Overlapping gene panels">{{panel_count}}
           </a>
-      {% endif %}
+        {% endif %}
+      </div>
+      {% endfor %}
+
     {% endif %}
   </div>
 {% endmacro %}
@@ -272,21 +290,20 @@
   ">
   {% if variant.clinsig_human %}
     <span class="badge bg-secondary">ClinVar</span>
-    <br>
   {% endif%}
   {% if variant.cosmic_ids %}
     <span class="badge bg-secondary">COSMIC</span>
-    <br>
+
   {% endif %}
   {% if variant.mitomap_associated_diseases %}
     <span class="badge bg-secondary">MITOMAP</span>
-    <br>
   {% endif %}
   {% if variant.clingen_cgh_pathogenic %}
-    <span class="badge bg-secondary">CGH Pathogenic</span><br>
+    <span class="badge bg-secondary">CGH Pathogenic</span>
   {% endif %}
   {% if variant.local_obs_old or variant.local_obs_cancer_germline_old or variant.local_obs_cancer_somatic_old %}
-    <span class="badge bg-secondary">Local</span>
+    <span class="badge bg-secondary">Local {% if variant.category in ['snv', 'sv'] %}<span class="badge bg-dark text-white">
+          {{ variant.local_obs_old or 0 }}</span>{% endif %}</span>
     <br>
   {% endif %}
   </div>

scout/server/blueprints/variants/templates/variants/mei-variants.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import mei_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell, variant_region_anno_cell %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - Mobile Element Insertion variants
@@ -65,7 +65,6 @@ onsubmit="return validateForm()">
               <th style="width:9%">Start loc</th>
               <th>Frequency</th>
               <th>Gene(s)</th>
-              <th>Region</th>
               <th>Function</th>
             </tr>
           </thead>
@@ -109,10 +108,7 @@ onsubmit="return validateForm()">
       {{ frequency_cell_general(variant) }}
     </td>
     <td>
-      {{ variant_gene_symbols_cell(variant) }}
-    </td>
-    <td style="word-wrap:break-word;">
-      {{ variant_region_anno_cell(variant) }}
+      {{ variant_gene_symbols_cell(variant, inherit_palette) }}
     </td>
     <td style="word-wrap:break-word;">
       {{ variant_funct_anno_cell(variant) }}

scout/server/blueprints/variants/templates/variants/str-variants.html

@@ -1,10 +1,11 @@
 {% extends "layout.html" %}
 {% from "utils.html" import comments_table, pedigree_panel %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general %}
 {% from "variant/buttons.html" import reviewer_button%}
-
+{% from "variant/gene_disease_relations.html" import inheritance_badge %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general %}
 {% from "variants/utils.html" import cell_rank, dismiss_variants_block, filter_form_footer, update_stash_filter_button_status, pagination_footer, pagination_hidden_div, str_filters, filter_script_main %}
 
+
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - STR variants
 {% endblock %}
@@ -239,6 +240,11 @@
   {% for gene in variant.genes %} {{ gene.symbol }} {% endfor %} {% endif %}
   </a>
   {% for gene in variant.genes %}
+      {% if variant.str_disease %}
+          {{ inheritance_badge(variant.str_inheritance_mode,inherit_palette) }}
+      {% else %}
+        {% for model in gene.inheritance %} {{ inheritance_badge(model,inherit_palette) }} {% endfor %}
+      {% endif %}
     <span class="badge bg-secondary"><a href="{{ gene.stripy_link }}" class="text-white" referrerpolicy="no-referrer" rel="noopener" target="_blank">S</a></span>
     <span class="badge bg-secondary"><a href="{{ gene.gnomad_str_link }}" class="text-white" referrerpolicy="no-referrer" rel="noopener" target="_blank">G</a></span>
   {% endfor %}

scout/server/blueprints/variants/templates/variants/sv-variants.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import sv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell, variant_region_anno_cell %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - SV variants
@@ -67,13 +67,12 @@ onsubmit="return validateForm()">
             <th>Pop Freq</th>
             <th>Observed</th>
             <th>Gene(s)</th>
-            <th>Region</th>
             <th>Function</th>
           </tr>
         </thead>
         <tbody>
           {% for variant in variants %}
-            {{ variant_row(variant) }}
+            {{ variant_row(variant, inherit_palette) }}
           {% else %}
             <tr>
                 <td colspan="11">No matching variants</td>
@@ -90,7 +89,7 @@ onsubmit="return validateForm()">
 </div>
 {% endblock %}
 
-{% macro variant_row(variant) %}
+{% macro variant_row(variant, inherit_palette) %}
   {% if variant.dismiss_variant %}
    <tr class="dismiss">
   {% elif 'causatives' in case and variant._id in case.causatives %}
@@ -114,10 +113,7 @@ onsubmit="return validateForm()">
     </td>
     <td>{{observed_cell_general(variant)}}</td>
     <td>
-      {{ variant_gene_symbols_cell(variant) }}
-    </td>
-    <td style="word-wrap:break-word;">
-      {{ variant_region_anno_cell(variant) }}
+      {{ variant_gene_symbols_cell(variant, inherit_palette) }}
     </td>
     <td style="word-wrap:break-word;">
       {{ variant_funct_anno_cell(variant) }}

scout/server/blueprints/variants/templates/variants/variants.html

@@ -56,16 +56,15 @@
             <tr>
               <th style="width:2%"></th>
               <th style="width:12%" title="Rank position">Rank</th>
-              <th style="width:4%" title="Rank score">Score</th>
+              <th style="width:5%" title="Rank score">Score</th>
               <th style="width:4%" title="Chromosome">Chr.</th>
-              <th style="width:8%" title="HGNC symbols">Gene</th>
-              <th style="width:4%" title="Pop Freq">Pop Freq</th>
-              <th style="width:6%" title="Observed database matches">Observed</th>
+              <th style="width:12%" title="HGNC symbols">Gene</th>
+              <th style="width:6%" title="Pop Freq">Pop Freq</th>
+              <th style="width:10%" title="Observed database matches">Observed</th>
               <th style="width:5%" title="CADD score">CADD</th>
-              <th style="width:8%" title="Gene region annotation">Gene annotation</th>
-              <th style="width:17%" title="Functional annotation">Func. annotation</th>
-              <th style="width:17%" title="Inheritance models">Inheritance model</th>
-              <th style="width:8%" title="Overlapping">Overlapping</th>
+              <th style="width:18%" title="Functional annotation">Function</th>
+              <th style="width:14%" title="Inheritance models">Inheritance model</th>
+              <th style="width:14%" title="Overlapping">Overlap</th>
             </tr>
          </thead>
          <tbody>
@@ -86,26 +85,19 @@
                     {{ mark_heteroplasmic_mt(case.individuals, variant.samples) }}
                   {% endif %}
 		            </td>
-                <td>{{ gene_cell(variant) }}</td>
+                <td>{{ gene_cell(variant, inherit_palette) }}</td>
                 <td class="text-start">{{ frequency_cell_general(variant) }}</td>
                 <td class="text-start">{{ observed_cell_general(variant) }}</td>
                 <td class="text-end">{{ cell_cadd(variant) }}</td>
                 <td>
-                  {% for annotation in variant.region_annotations %}
-                    <div>{{ annotation }}</div>
-                  {% endfor %}
-                </td>
-                <td>
-                  {% for annotation in variant.functional_annotations %}
-                    <div>{{ annotation }}</div>
-                  {% endfor %}
+                  {{ functional_annotation_cell(variant) }}
                 </td>
                 <td>{{ cell_models(variant) }}</td>
                 <td>{{ overlapping_cell(variant) }}</td>
               </tr>
             {% else %}
               <tr>
-                <td colspan="10">
+                <td colspan="9">
                   No matching variants
                 </td>
               </tr>
@@ -121,6 +113,19 @@
   </div>
 {% endblock %}
 
+{% macro functional_annotation_cell(variant) %}
+<div data-bs-toggle="tooltip" data-bs-html="true" title="
+  <div>
+    {% for annotation in variant.region_annotations %}
+          {{ annotation }}</br>
+    {% endfor %}
+  </div>">
+  {% for annotation in variant.functional_annotations %}
+      <div>{{ annotation }}</div>
+  {% endfor %}
+</div>
+{% endmacro %}
+
 {% macro cell_cadd(variant) %}
   <div data-bs-toggle="tooltip" data-bs-placement="left" data-bs-html="true" title="
     <div class='text-start'>

scout/server/blueprints/variants/views.py

@@ -13,6 +13,7 @@ from scout.constants import (
     CANCER_TIER_OPTIONS,
     DISMISS_VARIANT_OPTIONS,
     GENETIC_MODELS_PALETTE,
+    INHERITANCE_PALETTE,
     MANUAL_RANK_OPTIONS,
     SEVERE_SO_TERMS,
     SEVERE_SO_TERMS_SV,
@@ -163,6 +164,7 @@ def variants(institute_id, case_name):
         filters=available_filters,
         form=form,
         genetic_models_palette=GENETIC_MODELS_PALETTE,
+        inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
         manual_rank_options=MANUAL_RANK_OPTIONS,
         page=page,
@@ -254,6 +256,7 @@ def str_variants(institute_id, case_name):
         expand_search=controllers.get_expand_search(request.form),
         filters=available_filters,
         form=form,
+        inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
         manual_rank_options=MANUAL_RANK_OPTIONS,
         page=page,
@@ -333,6 +336,7 @@ def sv_variants(institute_id, case_name):
         expand_search=controllers.get_expand_search(request.form),
         filters=available_filters,
         form=form,
+        inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
         manual_rank_options=MANUAL_RANK_OPTIONS,
         page=page,
@@ -429,6 +433,7 @@ def mei_variants(institute_id, case_name):
         expand_search=controllers.get_expand_search(request.form),
         filters=available_filters,
         form=form,
+        inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
         manual_rank_options=MANUAL_RANK_OPTIONS,
         page=page,
@@ -627,6 +632,7 @@ def cancer_sv_variants(institute_id, case_name):
         expand_search=controllers.get_expand_search(request.form),
         filters=available_filters,
         form=form,
+        inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
         manual_rank_options=MANUAL_RANK_OPTIONS,
         page=page,

scout/utils/acmg.py

@@ -1,4 +1,12 @@
 # coding=UTF-8
+
+
+from typing import Optional
+
+from scout.constants import ACMG_COMPLETE_MAP
+from scout.constants.acmg import ACMG_POTENTIAL_CONFLICTS
+
+
 def is_pathogenic(pvs, ps_terms, pm_terms, pp_terms):
     """Check if the criterias for Pathogenic is fullfilled
 
@@ -157,38 +165,31 @@ def is_likely_benign(bs_terms, bp_terms):
     return False
 
 
-def get_acmg(acmg_terms):
-    """Use the algorithm described in ACMG paper to get a ACMG calssification
-
-    Modifying strength of a term is possible by adding a string describing its new level: "PP1_Strong" or
-    "PVS1_Moderate".
-
-    If no terms return None
-
-    Args:
-        acmg_terms(set(str)): A collection of prediction terms
-
-    Returns:
-        prediction(str): in ['uncertain_significance','benign','likely_benign',
-                             'likely_pathogenic','pathogenic']
-
+def get_acmg_criteria(acmg_terms: set) -> tuple:
     """
-    if not acmg_terms:
-        return None
-    prediction = "uncertain_significance"
-    # This variable indicates if Pathogenecity Very Strong exists
+    Given a set of ACMG evidence criteria terms, that may be strength modified with suffixes.
+    For each term,
+        first, Strength modified criteria suffixes should count towards their modified score.
+        then, we need to see if we match any of the two stand-alone terms. If so, set their respective booleans.
+        finally, check remaining prefixes if no suffix match or stand-alone criteria match
+
+    Return a tuple with
+        pvs: This variable indicates if Pathogenicity Very Strong exists
+        ps_terms: Collection of terms with Pathogenicity Strong
+        pm_terms: Collection of terms with Pathogenicity moderate
+        pp_terms: Collection of terms with Pathogenicity supporting
+        ba: This variable indicates if Benign impact stand-alone exists
+        bs_terms: Collection of terms with Benign evidence Strong
+        bp_terms: Collection of terms with supporting Benign evidence
+    """
+
     pvs = False
-    # Collection of terms with Pathogenecity Strong
     ps_terms = []
-    # Collection of terms with Pathogenecity moderate
     pm_terms = []
-    # Collection of terms with Pathogenecity supporting
     pp_terms = []
-    # This variable indicates if Benign impact stand-alone exists
+
     ba = False
-    # Collection of terms with Benign evidence Strong
     bs_terms = []
-    # Collection of terms with supporting Benign evidence
     bp_terms = []
 
     suffix_map = {
@@ -212,20 +213,51 @@ def get_acmg(acmg_terms):
                     if term.startswith(prefix):
                         term_list.append(term)
                         break
+                else:
+                    continue
                 break
         else:
-            # Do we match any of the two standalone terms
             if term.startswith("PVS"):
                 pvs = True
             elif term.startswith("BA"):
                 ba = True
-            else:  # Check remaining prefixes if no suffix match or standalone criteria match
+            else:
                 for prefix, term_list in prefix_map.items():
                     if term.startswith(prefix):
                         term_list.append(term)
                         break
 
-    # We need to start by checking for Pathogenecity
+    return (pvs, ps_terms, pm_terms, pp_terms, ba, bs_terms, bp_terms)
+
+
+def get_acmg(acmg_terms: set) -> Optional[str]:
+    """Use the algorithm described in ACMG paper (Richards 2015) to get a ACMG classification
+
+    Modifying strength of a term is possible by adding a string describing its new level: "PP1_Strong" or
+    "PVS1_Moderate".
+
+    BA is considered fully Stand Alone.
+
+    If no terms return None
+
+    Args:
+        acmg_terms(set(str)): A collection of prediction terms
+
+    Returns:
+        prediction(str): in ['uncertain_significance','benign','likely_benign',
+                             'likely_pathogenic','pathogenic']
+
+    """
+    if not acmg_terms:
+        return None
+
+    (pvs, ps_terms, pm_terms, pp_terms, ba, bs_terms, bp_terms) = get_acmg_criteria(acmg_terms)
+
+    if ba:
+        return "benign"
+
+    prediction = "uncertain_significance"
+
     pathogenic = is_pathogenic(pvs, ps_terms, pm_terms, pp_terms)
     likely_pathogenic = is_likely_pathogenic(pvs, ps_terms, pm_terms, pp_terms)
     benign = is_benign(ba, bs_terms)
@@ -245,3 +277,98 @@ def get_acmg(acmg_terms):
             prediction = "likely_benign"
 
     return prediction
+
+
+def get_acmg_temperature(acmg_terms: set) -> Optional[dict]:
+    """
+    Use the algorithm described in Tavtigian 2020 to classifiy variants.
+
+    PVS 8 points, S 4, M 2, P 1.
+    This gives:
+
+    P > 10
+    LP 6 < p < 9
+    VUS 0 < p < 5
+    LB -1 < p < -6
+    B < -7
+
+    If no terms return None
+
+    Args:
+        acmg_terms(set(str)): A collection of prediction terms
+
+    Returns:
+        dict:
+            temperature:
+        (points, temperature, point_classification)
+
+    """
+    TEMPERATURE_STRINGS = {
+        -1: {"label": "B/LB", "color": "success", "icon": "fa-times"},
+        0: {"label": "Ice cold", "color": "info", "icon": "fa-icicles"},
+        1: {"label": "Cold", "color": "info", "icon": "fa-snowman"},
+        2: {"label": "Cold", "color": "info", "icon": "fa-snowflake"},
+        3: {"label": "Tepid", "color": "yellow", "icon": "fa-temperature-half"},
+        4: {"label": "Warm", "color": "orange", "icon": "fa-mug-hot"},
+        5: {"label": "Hot", "color": "red", "icon": "fa-pepper-hot"},
+        6: {"label": "LP/P", "color": "danger", "icon": "fa-stethoscope"},
+    }
+
+    if not acmg_terms:
+        return {}
+
+    (pvs, ps_terms, pm_terms, pp_terms, ba, bs_terms, bp_terms) = get_acmg_criteria(acmg_terms)
+
+    if ba:
+        points = -8
+    else:
+        points = (
+            8 * pvs
+            + 4 * len(ps_terms)
+            + 2 * len(pm_terms)
+            + len(pp_terms)
+            - 4 * len(bs_terms)
+            - len(bp_terms)
+        )
+
+    if points <= -7:
+        point_classification = "benign"
+        temperature_icon = TEMPERATURE_STRINGS[-1].get("icon")
+    elif points <= -1:
+        point_classification = "likely_benign"
+        temperature_icon = TEMPERATURE_STRINGS[-1].get("icon")
+    elif points <= 5:
+        point_classification = "uncertain_significance"
+    elif points <= 9:
+        point_classification = "likely_pathogenic"
+        temperature_icon = TEMPERATURE_STRINGS[6].get("icon")
+    elif points >= 10:
+        point_classification = "pathogenic"
+        temperature_icon = TEMPERATURE_STRINGS[6].get("icon")
+
+    temperature_class = ACMG_COMPLETE_MAP[point_classification].get("color")
+    temperature = ACMG_COMPLETE_MAP[point_classification].get("label")
+
+    if point_classification == "uncertain_significance":
+        temperature_class = TEMPERATURE_STRINGS[points].get("color")
+        temperature = TEMPERATURE_STRINGS[points].get("label")
+        temperature_icon = TEMPERATURE_STRINGS[points].get("icon")
+
+    return {
+        "points": points,
+        "temperature": temperature,
+        "temperature_class": temperature_class,
+        "temperature_icon": temperature_icon,
+        "point_classification": ACMG_COMPLETE_MAP[point_classification].get("short"),
+    }
+
+
+def get_acmg_conflicts(acmg_terms: set) -> list:
+    """Check potential conflict paris, return list of reference strings."""
+
+    conflicts = []
+    for t1, t2, reference in ACMG_POTENTIAL_CONFLICTS:
+        if t1 in acmg_terms and t2 in acmg_terms:
+            conflicts.append(reference)
+
+    return conflicts

scout/utils/scout_requests.py

@@ -3,7 +3,7 @@
 import logging
 import urllib.request
 import zlib
-from typing import Dict
+from typing import Dict, List
 from urllib.error import HTTPError
 
 import requests
@@ -134,7 +134,7 @@ def fetch_resource(url, json=False):
     """
     if url.startswith("ftp"):
         # requests do not handle ftp
-        response = urllib.request.urlopen(url, timeout=TIMEOUT)
+        response = urllib.request.urlopen(url, timeout=TIMEOUT)  # nosec
         if isinstance(response, Exception):
             raise response
         data = response.read().decode("utf-8")
@@ -307,20 +307,15 @@ def fetch_orpha_files() -> Dict:
     return orpha_files
 
 
-def fetch_hgnc():
-    """Fetch the hgnc genes file from
-        ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
-
-    Returns:
-        hgnc_gene_lines(list(str))
+def fetch_hgnc() -> List[str]:
+    """Fetch the hgnc genes names file from
+    https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
     """
-    file_name = "hgnc_complete_set.txt"
-    url = "ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/{0}".format(file_name)
-    LOG.info("Fetching HGNC genes from %s", url)
 
-    hgnc_lines = fetch_resource(url)
+    url = "https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt"
+    LOG.info("Fetching HGNC genes from %s", url)
 
-    return hgnc_lines
+    return fetch_resource(url)
 
 
 def fetch_constraint():

{scout_browser-4.89.1.dist-info → scout_browser-4.90.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.89.1
+Version: 4.90
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson