scout-browser 4.84__py3-none-any.whl → 4.86__py3-none-any.whl

scout/parse/variant/transcript.py

@@ -324,7 +324,7 @@ def set_variant_frequencies(transcript, entry):
                 continue
 
             value = entry[key]
-            if not value or value == ".":
+            if not value or value == "." or value.isalpha():
                 continue
 
             if key in THOUSAND_GENOMES_CSQ_KEYS:

scout/parse/variant/variant.py

@@ -231,10 +231,7 @@ def parse_variant(
         parsed_variant["revel_score"] = parsed_transcripts[0].get(
             "revel_rankscore"
         )  # This is actually the value of REVEL_rankscore
-
-        parsed_variant["revel"] = parsed_transcripts[0].get(
-            "revel_raw_score"
-        )  # This is actually the value of REVEL_score
+        parsed_variant["revel"] = get_highest_revel_score(parsed_transcripts)
 
     ###################### Add conservation ######################
     parsed_variant["conservation"] = parse_conservations(variant, parsed_transcripts)
@@ -261,6 +258,15 @@ def parse_variant(
     return parsed_variant
 
 
+def get_highest_revel_score(parsed_transcripts: List[dict]) -> Optional[float]:
+    """Retrieve the highest REVEL_score value from parsed variant transcripts."""
+    tx_revel_scores: List(float) = [
+        tx.get("revel_raw_score") for tx in parsed_transcripts if tx.get("revel_raw_score") != None
+    ]
+    if tx_revel_scores:
+        return max(tx_revel_scores)
+
+
 def get_genmod_key(case):
     """Gen genmod key
 

scout/server/app.py

@@ -7,7 +7,7 @@ from typing import Dict, Union
 from urllib.parse import parse_qsl, unquote, urlsplit
 
 import coloredlogs
-from flask import Flask, current_app, redirect, request, url_for
+from flask import Flask, redirect, request, url_for
 from flask_cors import CORS
 from flask_login import current_user
 from markdown import markdown as python_markdown
@@ -25,6 +25,7 @@ from .blueprints import (
     institutes,
     login,
     managed_variants,
+    omics_variants,
     panels,
     phenomodels,
     phenotypes,
@@ -98,6 +99,7 @@ def configure_extensions(app):
     extensions.store.init_app(app)
     extensions.login_manager.init_app(app)
     extensions.mail.init_app(app)
+    extensions.clinvar_api.init_app(app)
 
     if app.config.get("SQLALCHEMY_DATABASE_URI"):
         extensions.chanjo_report.init_app(app)
@@ -177,6 +179,7 @@ def register_blueprints(app):
     app.register_blueprint(diagnoses.omim_bp)
     app.register_blueprint(institutes.overview)
     app.register_blueprint(managed_variants.managed_variants_bp)
+    app.register_blueprint(omics_variants.omics_variants_bp)
 
 
 def register_filters(app):

scout/server/blueprints/alignviewers/controllers.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 import logging
 import os.path
-from typing import Dict
+from typing import Dict, Optional
 
 from flask import flash, session
 from flask_login import current_user
@@ -12,7 +12,7 @@ from scout.server.utils import case_append_alignments, find_index
 from scout.utils.ensembl_rest_clients import EnsemblRestApiClient
 
 LOG = logging.getLogger(__name__)
-CUSTOM_TRACK_NAMES = ["Genes", "ClinVar", "ClinVar CNVs"]
+DEFAULT_TRACK_NAMES = ["Genes", "ClinVar", "ClinVar CNVs"]
 
 
 def check_session_tracks(resource):
@@ -51,33 +51,39 @@ def set_session_tracks(display_obj: dict):
     session["igv_tracks"] = session_tracks
 
 
-def make_igv_tracks(case_obj, variant_id, chrom=None, start=None, stop=None):
+def make_igv_tracks(
+    case_obj: dict,
+    variant_id: str,
+    chrom: Optional[str] = None,
+    start: Optional[int] = None,
+    stop: Optional[int] = None,
+) -> dict:
     """Create a dictionary containing the required tracks for displaying IGV tracks for case or a group of cases
 
     Args:
-        institute_id(str): institute _id
+        institute_id: institute _id
         case_obj(scout.models.Case)
-        variant_id(str): _id of a variant
-        chrom(str/None): requested chromosome [1-22], X, Y, [M-MT]
-        start(int/None): start of the genomic interval to be displayed
-        stop(int/None): stop of the genomic interval to be displayed
+        variant_id: _id of a variant
+        chrom: requested chromosome [1-22], X, Y, [M-MT]
+        start: start of the genomic interval to be displayed
+        stop: stop of the genomic interval to be displayed
 
     Returns:
-        display_obj(dict): A display object containing case name, list of genes, lucus and tracks
+        display_obj: A display object containing case name, list of genes, locus and tracks
     """
     display_obj = {}
     variant_obj = store.variant(document_id=variant_id)
 
+    chromosome = "All"
     if variant_obj:
         # Set display locus
         start = start or variant_obj["position"]
         stop = stop or variant_obj["end"]
+        chrom = chrom or variant_obj.get("chromosome")
 
-        chromosome = chrom or variant_obj.get("chromosome")
-        chromosome = chromosome.replace("MT", "M")
+    if all([start, stop, chrom]):
+        chromosome = chrom.replace("MT", "M")
         display_obj["locus"] = "chr{0}:{1}-{2}".format(chromosome, start, stop)
-    else:
-        chromosome = "All"
 
     # Set genome build for displaying alignments:
     if "38" in str(case_obj.get("genome_build", "37")) or chromosome == "M":
@@ -115,20 +121,27 @@ def make_igv_tracks(case_obj, variant_id, chrom=None, start=None, stop=None):
     return display_obj
 
 
-def make_sashimi_tracks(case_obj, variant_id=None):
+def make_sashimi_tracks(
+    case_obj: dict, variant_id: Optional[str] = None, omics_variant_id: Optional[str] = None
+):
     """Create a dictionary containing the required tracks for a splice junction plot
+    If either a regular variant_id or an omics variant id is passed, set display to a particular locus.
+    Otherwise defaults to whole genome "All" view.
 
-    Args:
-        case_obj(scout.models.Case)
-        variant_id(str) _id of a variant
     Returns:
-        display_obj(dict): A display object containing case name, list of genes, lucus and tracks
+        display_obj(dict): A display object containing case name, list of genes, locus and tracks
     """
     build = "38"  # This feature is only available for RNA tracks in build 38
 
     locus = "All"
+    variant_obj = None
+
     if variant_id:
         variant_obj = store.variant(document_id=variant_id)
+    if omics_variant_id:
+        variant_obj = store.omics_variant(variant_id=omics_variant_id)
+
+    if variant_obj:
         locus = make_locus_from_variant(variant_obj, case_obj, build)
 
     display_obj = {"locus": locus, "tracks": []}
@@ -234,9 +247,9 @@ def set_common_tracks(display_obj, build):
     # Set up IGV tracks that are common for all cases:
     display_obj["reference_track"] = HUMAN_REFERENCE[build]  # Human reference is always present
 
-    # if user settings for igv tracks exist -> use these settings, otherwise display all tracks
+    # if user settings for igv tracks exist -> use these settings, otherwise display default tracks ---> Genes, ClinVar and ClinVar CNVs
     custom_tracks_names = (
-        user_obj.get("igv_tracks") if "igv_tracks" in user_obj else CUSTOM_TRACK_NAMES
+        user_obj.get("igv_tracks") if "igv_tracks" in user_obj else DEFAULT_TRACK_NAMES
     )
 
     display_obj["custom_tracks"] = []
@@ -300,7 +313,6 @@ def set_config_custom_tracks(display_obj: dict, build: str):
     """Set up custom public or private tracks stored in a cloud bucket or locally. These tracks were those specified in the Scout config file.
     Respect user's preferences."""
     user_obj = store.user(email=current_user.email)
-    custom_tracks_names = user_obj.get("igv_tracks")
 
     config_custom_tracks = []
 
@@ -308,8 +320,7 @@ def set_config_custom_tracks(display_obj: dict, build: str):
         build_tracks = config_igv_tracks.tracks.get(build, [])
         for track in build_tracks:
             # Do not display track if user doesn't want to see it
-            if custom_tracks_names and track["name"] not in custom_tracks_names:
-                continue
-            config_custom_tracks.append(track)
+            if "igv_tracks" not in user_obj or track["name"] in user_obj.get("igv_tracks"):
+                config_custom_tracks.append(track)
     if config_custom_tracks:
         display_obj["config_custom_tracks"] = config_custom_tracks

scout/server/blueprints/alignviewers/templates/alignviewers/igv_sashimi_viewer.html

@@ -79,6 +79,7 @@
                                     type: 'wig',
                                     format: "bigwig",
                                     url: "{{ url_for('alignviewers.remote_static', file=track.coverage_wig) }}",
+                                    height: 500,
                                   },
                                   {
                                     type: 'spliceJunctions',
@@ -88,24 +89,27 @@
                                     labelUniqueReadCount: true,
                                     url: "{{ url_for('alignviewers.remote_static', file=track.splicej_bed) }}",
                                     indexURL: "{{ url_for('alignviewers.remote_static', file=track.splicej_bed_index) }}",
-                                    minUniquelyMappedReads: 1
+                                    minUniquelyMappedReads: 1,
+                                    height: 500,
                                   },
                                 ]
                               }, // end of sashimi track with data
-                              { // genes track
-                                name: geneTrack.name,
-                                type: geneTrack.type,
-                                format: geneTrack.format,
-                                sourceType: geneTrack.sourceType,
-                                url: geneTrack.url,
-                                indexURL: geneTrack.indexURL,
-                                displayMode: geneTrack.displayMode,
-                                visibilityWindow: 300000000,
-                                height: 100,
-                                searchable: true,
-                                order: {{counter.loop}},
-                                infoURL: "https://www.ncbi.nlm.nih.gov/gene/?term=$$"
-                              }, // end of genes track
+                              {% if custom_tracks|selectattr("name","equalto", "Genes")|list|length > 0 %}
+                                { // genes track
+                                  name: geneTrack.name,
+                                  type: geneTrack.type,
+                                  format: geneTrack.format,
+                                  sourceType: geneTrack.sourceType,
+                                  url: geneTrack.url,
+                                  indexURL: geneTrack.indexURL,
+                                  displayMode: geneTrack.displayMode,
+                                  visibilityWindow: 300000000,
+                                  height: 100,
+                                  searchable: true,
+                                  order: {{counter.loop}},
+                                  infoURL: "https://www.ncbi.nlm.nih.gov/gene/?term=$$"
+                                }, // end of genes track
+                              {% endif %}
                             {% endif %}
                         {% endfor %}
                     ] // end of tracks

scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html

@@ -14,14 +14,11 @@
     <link rel="stylesheet" type="text/css"
           href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/themes/smoothness/jquery-ui.css"/>
 
-    <!-- Font Awesome CSS -->
-    <link rel="stylesheet" type="text/css"
-          href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css"/>
-
     <!-- jQuery JS -->
     <script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
     <script type="text/javascript"
             src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js"></script>
+
     {{ igv_script() }}
 </head>
 
@@ -30,6 +27,11 @@
 </body>
 
 <script type="text/javascript">
+
+  var outLinks = {
+    COSV: "https://cancer.sanger.ac.uk/cosmic/search?q=", // COSMIC variant search
+  };
+
   $(document).ready(function () {
       var div = $("#igvDiv")[0],
               options = {
@@ -146,7 +148,45 @@
                       {% endfor %}
                   ]
               };
-      igv.createBrowser(div, options);
+      igv.createBrowser(div, options)
+      .then(function (browser) {
+          browser.on('trackclick', function (track, popoverData) {
+
+              var markup = "<table class=\"igv-popover-table\">";
+
+              // Don't show a pop-over when there's no data.
+              if (!popoverData || !popoverData.length) {
+                  return false;
+              }
+
+              popoverData.forEach(function (nameValue) {
+
+              if (nameValue.name) {
+
+                  var value = nameValue.value;
+                  for (var key in outLinks) {
+                    if (nameValue.value.toString().startsWith(key) && nameValue.name.toLowerCase() === 'name') {
+                      value = '<a href="' + outLinks[key] + value + '" target="_blank" rel="noopener noreferrer">' + nameValue.value + '</a>';
+                    }
+                  }
+
+                  markup += "<tr><td class=\"igv-popover-td\">"
+                          + "<span class=\"igv-popover-name\">" + nameValue.name + "</span>&nbsp;"
+                          + "<span class=\"igv-popover-value\">" + value + "</span>"
+                          + "</td></tr>";
+                  }
+                  else {
+                      // not a name/value pair
+                      markup += "<tr><td>" + nameValue.toString() + "</td></tr>";
+                  }
+                });
+
+                markup += "</table>";
+
+              // By returning a string from the trackclick handler we're asking IGV to use our custom HTML in its pop-over.
+              return markup;
+          });
+      });
   });
 </script>
 

scout/server/blueprints/alignviewers/templates/alignviewers/utils.html

@@ -1,5 +1,5 @@
 {% macro igv_script() %}
   <link rel="shortcut icon" href="//igv.org/web/img/favicon.ico">
   <!-- IGV JS-->
-  <script src="https://cdn.jsdelivr.net/npm/igv@2.15.11/dist/igv.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/igv@3.0.1/dist/igv.min.js"></script>
 {% endmacro %}

scout/server/blueprints/alignviewers/views.py

@@ -91,7 +91,15 @@ def remote_static():
 @alignviewers_bp.route(
     "/<institute_id>/<case_name>/<variant_id>/igv-splice-junctions", methods=["GET"]
 )
-def sashimi_igv(institute_id, case_name, variant_id=None):
+@alignviewers_bp.route(
+    "/<institute_id>/<case_name>/outliers/<omics_variant_id>/igv-splice-junctions", methods=["GET"]
+)
+def sashimi_igv(
+    institute_id: str,
+    case_name: str,
+    variant_id: Optional[str] = None,
+    omics_variant_id: Optional[str] = None,
+):
     """Visualize splice junctions on igv.js sashimi-like viewer for one or more individuals of a case.
     wiki: https://github.com/igvteam/igv.js/wiki/Splice-Junctions
     """
@@ -99,7 +107,7 @@ def sashimi_igv(institute_id, case_name, variant_id=None):
         store, institute_id, case_name
     )  # This function takes care of checking if user is authorized to see resource
 
-    display_obj = controllers.make_sashimi_tracks(case_obj, variant_id)
+    display_obj = controllers.make_sashimi_tracks(case_obj, variant_id, omics_variant_id)
     controllers.set_session_tracks(display_obj)
 
     response = Response(render_template("alignviewers/igv_sashimi_viewer.html", **display_obj))

scout/server/blueprints/cases/controllers.py

@@ -64,6 +64,7 @@ JSON_HEADERS = {
 COVERAGE_REPORT_TIMEOUT = 20
 
 PANEL_PROJECTION = {"version": 1, "display_name": 1, "genes": 1}
+PANEL_HIDDEN_PROJECTION = {"version": 1, "display_name": 1, "hidden": 1}
 
 
 def phenomizer_diseases(hpo_ids, case_obj, p_value_treshold=1):
@@ -339,6 +340,8 @@ def case(
 
     case_obj["default_genes"] = _get_default_panel_genes(store, case_obj)
 
+    _set_panel_removed(store, case_obj)
+
     for hpo_term in itertools.chain(
         case_obj.get("phenotype_groups") or [], case_obj.get("phenotype_terms") or []
     ):
@@ -449,6 +452,9 @@ def case(
         "gens_info": gens.connection_settings(case_obj.get("genome_build")),
         "display_rerunner": rerunner.connection_settings.get("display", False),
         "hide_matching": hide_matching,
+        "audits": store.case_events_by_verb(
+            category="case", institute=institute_obj, case=case_obj, verb="filter_audit"
+        ),
     }
 
     return data
@@ -479,6 +485,18 @@ def _limit_genes_on_default_panels(default_genes: list, limit_genes: list) -> li
     return list(default_genes_set.intersection(limit_genes_set))
 
 
+def _set_panel_removed(store: MongoAdapter, case_obj: dict) -> list:
+    """Flag panel on list removed if the latest panel version is marked hidden."""
+
+    for panel_info in case_obj.get("panels", []):
+        latest_panel = store.gene_panel(
+            panel_info["panel_name"], projection=PANEL_HIDDEN_PROJECTION
+        )
+        panel_info["removed"] = (
+            latest_panel.get("hidden", False) if latest_panel is not None else False
+        )
+
+
 def _get_default_panel_genes(store: MongoAdapter, case_obj: dict) -> list:
     """Get unique genes on case default panels.
 
@@ -510,7 +528,6 @@ def _get_default_panel_genes(store: MongoAdapter, case_obj: dict) -> list:
             projection=PANEL_PROJECTION,
         )
         latest_panel = store.gene_panel(panel_name, projection=PANEL_PROJECTION)
-        panel_info["removed"] = False if latest_panel is None else latest_panel.get("hidden", False)
         if not panel_obj:
             panel_obj = latest_panel
             if not panel_obj:

scout/server/blueprints/cases/templates/cases/case.html

@@ -1,7 +1,7 @@
 {% extends "layout.html" %}
 {% from "cases/collapsible_actionbar.html" import action_bar, research_modal, reanalysis_modal %}
 {% from "utils.html" import comments_panel, activity_panel, pedigree_panel %}
-{% from "cases/utils.html" import causatives_list, suspects_list, remove_form, matching_causatives, matching_managed_variants, beacon_modal, matchmaker_modal %}
+{% from "cases/utils.html" import causatives_list, suspects_list, remove_form, matching_causatives, matching_managed_variants, beacon_modal, matchmaker_modal, filter_audits %}
 {% from "cases/individuals_table.html" import cancer_individuals_table, individuals_table %}
 {% from "cases/phenotype.html" import hpo_item, cohort_panel, diagnosis_phenotypes, phenotype_groups_panel, add_phenotype_terms_panel, hpo_panel %}
 {% from "cases/gene_panel.html" import genepanels_table, hpo_genelist_panel %}
@@ -119,8 +119,16 @@
         </div>
       </div>
 
+      <div class="row ms-1">
       {{ matching_variants() }}
 
+      {% if audits | count_cursor > 0 %}
+        <div class="card panel-default col-4 ms-5 me-1">
+            {{ filter_audits(audits, true) }}
+        </div>
+      {% endif %}
+      </div>
+
       <div class="card panel-default" >
         <div class="row">
           <div class="col">{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}</div>
@@ -258,6 +266,9 @@
         {% if case.vcf_files.vcf_fusion %}
           <a class="btn btn-dark btn-sm text-white" href="{{ url_for('variants.fusion_variants', institute_id=institute._id, case_name=case.display_name, variant_type='clinical') }}">Clinical fusion variants</a>
         {% endif %}
+        {% if case.has_outliers %}
+          <a class="btn btn-dark btn-sm text-white" href="{{ url_for('omics_variants.outliers', institute_id=institute._id, case_name=case.display_name, variant_type='clinical') }}">Clinical WTS outliers</a>
+        {% endif %}
       </div>
     </div>
   </div>
@@ -352,7 +363,7 @@
                   <a href="{{ url_for('cases.case', institute_id=grouped_case.owner, case_name=grouped_case.display_name) }}">{{ grouped_case.display_name }}</a>
 
                   <a href="{{ url_for('cases.remove_case_group', institute_id=institute._id, case_name=grouped_case.display_name, case_group=group_id) }}" class="btn btn-link btn-sm">
-                      <span class="fa fa-remove text-dark"></span></a>
+                      <span class="fa fa-times text-dark"></span></a>
 
                 </div>
               {% endfor %}
@@ -537,9 +548,9 @@
 {% endmacro %}
 
 {% macro matching_variants() %}
-<div class="card mt-3">
-  <div class="row mt-0 ms-3">
-    <div class="col-sm-12 col-md-12">
+<div class="card mt-3 col-7">
+  <div class="mt-0">
+    <div class="col-md-7">
       <div data-bs-toggle='tooltip' class="panel-heading" title="Check if there are any variants in this case
         marked as causative in another case for this institute, or are on the managed variants list.">
         <strong>
@@ -554,27 +565,27 @@
     {% if hide_matching == false %}
       {% if other_causatives|length > 0 %}
         <div class="row mt-0 ms-3">
-          <div class="col-xs-12 col-md-12">{{ matching_causatives(other_causatives, institute, case) }}</div>
+          <div class="col-md-7">{{ matching_causatives(other_causatives, institute, case) }}</div>
         </div>
       {% endif %}
       {% if default_other_causatives|length > 0%}
         <div class="row mt-0 ms-3">
-          <div class="col-xs-12 col-md-12">{{ matching_causatives(default_other_causatives, institute, case, default=True) }}</div>
+          <div class="col-md-7">{{ matching_causatives(default_other_causatives, institute, case, default=True) }}</div>
         </div>
       {% endif %}
       {% if managed_variants|length > 0%}
         <div class="row mt-0 ms-3">
-          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(managed_variants, institute, case) }}</div>
+          <div class="col-md-7">{{ matching_managed_variants(managed_variants, institute, case) }}</div>
         </div>
       {% endif %}
       {% if default_managed_variants|length > 0%}
         <div class="row mt-0 ms-3">
-          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
+          <div class="col-md-7">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
         </div>
       {% endif %}
       {% if other_causatives|length == 0 and default_other_causatives|length == 0 and managed_variants|length == 0 and default_managed_variants|length == 0%}
         <div class="row mt-0 ms-3">
-          <div class="col-sm-12 col-md-12">No matching causatives or managed variants found</div>
+          <div class="col-md-7">No matching causatives or managed variants found</div>
         </div>
       {% endif %}
     {% endif %}
@@ -772,5 +783,12 @@ $('#collapse-icon').addClass('fa-angle-double-left');
 $('[data-bs-toggle=sidebar-collapse]').click(function() {
   SidebarCollapse();
 });
+
+function dynamicPhenotypeCheck(source){
+  var checkboxes = document.getElementsByName('hpo_id');
+  for(var i=0, n=checkboxes.length;i<n;i++) {
+    checkboxes[i].checked = source.checked;
+  }
+}
 </script>
 {% endblock %}

scout/server/blueprints/cases/templates/cases/case_report.html

@@ -1,4 +1,4 @@
-{% from "cases/utils.html" import variant_transcripts %}
+{% from "cases/utils.html" import variant_transcripts, filter_audits %}
 {% from "utils.html" import comments_table, variant_related_comments_table %}
 {% from "variants/components.html" import fusion_variants_header, default_fusion_variant_cells %}
 
@@ -266,22 +266,7 @@
         {% if audits | count_cursor > 0 %}
         <tr>
           <td colspan=2>
-            <table id="audit-table" class="table table-sm" style="background-color: transparent">
-              <thead>
-                <tr>
-                  <th>Filters marked audited for case</th>
-                </tr>
-              </thead>
-              <tbody>
-                 {% set audit_query = namespace() %}
-                 {% for audit in audits %}
-                  {% set audit_query = audit.link|url_args %}
-                  <tr>
-                    <td><strong>{{ audit.subject }} ({{audit_query.variant_type if audit_query.variant_type else "type unavailable -"}} {{ audit_query.category if audit_query.category else "category unavailable"}})</strong> was marked checked by {{ audit.user_name }} on {{audit.created_at.strftime('%Y-%m-%d')}}.</td>
-                  </tr>
-                 {%  endfor %}
-              </tbody>
-            </table>
+            {{filter_audits(audits)}}
           </td>
         </tr>
         {% endif %}

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html

@@ -247,7 +247,7 @@
             {% else %}
               <button type="submit" name="action" value="DELETE" class="btn btn-warning btn-xs form-control">
             {% endif %}
-                <span class="fa fa-remove"></span>
+                <span class="fa fa-times"></span>
                   {{ user.name }}
               </button>
         </form>