scout-browser 4.84__tar.gz → 4.85__tar.gz

{scout-browser-4.84 → scout-browser-4.85}/CHANGELOG.md

@@ -4,6 +4,19 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.85]
+### Added
+- Load also genes which are missing Ensembl gene ID (72 in both builds), including immunoglobulins and fragile sites
+### Changed
+- Unfreeze werkzeug again
+- Show "(Removed)" after removed panels in dropdown
+- The REVEL score is collected as the maximum REVEL score from all of the variant's transcripts
+- Parse GNOMAD POPMAX values only if they are numerical when loading variants
+### Fixed
+- Alphabetically sort "select default panels" dropdown menu options on case page
+- Show gene panel removed status on case page
+- Fixed visibility of the following buttons: remove assignee, remove pinned/causative, remove comment, remove case from group
+
 ## [4.84]
 ### Changed
 - Clearer error message when a loqusdb query fails for an instance that initially connected

{scout-browser-4.84/scout_browser.egg-info → scout-browser-4.85}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.84
+Version: 4.85
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

{scout-browser-4.84 → scout-browser-4.85}/requirements.txt

@@ -1,5 +1,5 @@
 # Everything needed in production
-werkzeug<3
+werkzeug
 Flask>=2.0
 Flask-Bootstrap
 Flask-CORS

scout-browser-4.85/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.85"

{scout-browser-4.84 → scout-browser-4.85}/scout/adapter/mongo/cytoband.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import logging
+from typing import Dict
 
 import pymongo
 
@@ -20,6 +21,18 @@ class CytobandHandler(object):
         result = self.cytoband_collection.insert_many(cytobands)
         LOG.debug(f"Number of inserted documents:{len(result.inserted_ids)}")
 
+    def cytoband_to_coordinates(self, build: str) -> Dict[str, dict]:
+        """Returns a dictionary with cytoband name as key and its coordinates as value."""
+        cytobands = self.cytoband_collection.find({"build": build})
+        return {
+            "".join([cytoband["chrom"], cytoband["band"]]): {
+                "chromosome": cytoband["chrom"],
+                "start": int(cytoband["start"]),
+                "stop": int(cytoband["stop"]),
+            }
+            for cytoband in cytobands
+        }
+
     def cytoband_by_chrom(self, build="37"):
         """Returns a dictionary of cytobands with chromosomes as keys
 

{scout-browser-4.84 → scout-browser-4.85}/scout/adapter/mongo/hgnc.py

@@ -405,7 +405,7 @@ class GeneHandler(object):
             add_transcripts = True
 
         for gene_obj in self.all_genes(build=build, add_transcripts=add_transcripts):
-            ensg_id = gene_obj["ensembl_id"]
+            ensg_id = gene_obj.get("ensembl_id")
             hgnc_id = gene_obj["hgnc_id"]
             transcript_objs = gene_obj.get("ens_transcripts")
             if id_transcripts and transcript_objs:

{scout-browser-4.84 → scout-browser-4.85}/scout/commands/update/genes.py

@@ -30,6 +30,9 @@ from scout.load import load_hgnc_genes, load_transcripts
 from scout.server.extensions import store
 from scout.utils.handle import get_file_handle
 
+ENSEMBL_GENE_RESOURCES = {"37": "ensembl_genes_37", "38": "ensembl_genes_38"}
+ENSEMBL_TX_RESOURCES = {"37": "ensembl_transcripts_37", "38": "ensembl_transcripts_38"}
+
 LOG = logging.getLogger(__name__)
 
 
@@ -137,7 +140,7 @@ def genes(build, downloads_folder, api_key):
             except Exception as ex:
                 LOG.error(ex)
             fetch_downloaded_resources(resources, tempdir, builds)
-    else:  # If resources have been previosly downloaded, read those file and return their lines
+    else:  # If resources have been previously downloaded, read those file and return their lines
         fetch_downloaded_resources(resources, downloads_folder, builds)
 
     # Load genes and transcripts info
@@ -147,11 +150,7 @@ def genes(build, downloads_folder, api_key):
         LOG.warning("Dropping all transcript information")
         adapter.drop_transcripts(genome_build)
 
-        ensembl_gene_res = (
-            resources.get("ensembl_genes_37")
-            if genome_build == "37"
-            else resources.get("ensembl_genes_38")
-        )  # It will be none if everything needs to be downloaded
+        ensembl_gene_res = resources.get(ENSEMBL_GENE_RESOURCES[genome_build])
 
         # Load the genes
         hgnc_genes = load_hgnc_genes(
@@ -167,15 +166,12 @@ def genes(build, downloads_folder, api_key):
 
         ensembl_genes_dict = {}
         for gene_obj in hgnc_genes:
-            ensembl_id = gene_obj["ensembl_id"]
-            ensembl_genes_dict[ensembl_id] = gene_obj
+            if gene_obj.get("ensembl_id"):
+                ensembl_id = gene_obj["ensembl_id"]
+                ensembl_genes_dict[ensembl_id] = gene_obj
 
         # Load the transcripts
-        ensembl_tx_res = (
-            resources.get("ensembl_transcripts_37")
-            if genome_build == "37"
-            else resources.get("ensembl_transcripts_38")
-        )  # It will be none if everything needs to be downloaded
+        ensembl_tx_res = resources.get(ENSEMBL_TX_RESOURCES[genome_build])
 
         load_transcripts(adapter, ensembl_tx_res, genome_build, ensembl_genes_dict)
 

{scout-browser-4.84 → scout-browser-4.85}/scout/load/hgnc_gene.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import logging
+from typing import Dict
 
 from click import progressbar
 
@@ -16,6 +17,22 @@ from scout.utils.scout_requests import (
 LOG = logging.getLogger(__name__)
 
 
+def set_missing_gene_coordinates(gene_data: dict, cytoband_coords: Dict[str, dict]):
+    """Attempt at collecting gene coordinates from cytoband for genes missing Ensembl ID."""
+
+    if gene_data.get("ensembl_gene_id") not in [
+        "",
+        None,
+    ]:  # Coordinates are present, since they're collected from the Ensembl file
+        return
+    gene_data["ensembl_gene_id"] = None
+    cytoband_coord: dict = cytoband_coords.get(gene_data["location"])
+    if cytoband_coord:
+        gene_data["chromosome"]: str = cytoband_coord["chromosome"]
+        gene_data["start"]: int = cytoband_coord["start"]
+        gene_data["end"]: int = cytoband_coord["stop"]
+
+
 def load_hgnc_genes(
     adapter,
     genes=None,
@@ -36,7 +53,7 @@ def load_hgnc_genes(
     Args:
         adapter(scout.adapter.MongoAdapter)
         genes(dict): If genes are already parsed
-        ensembl_lines(iterable(str)): Lines formated with ensembl gene information
+        ensembl_lines(iterable(str)): Lines formatted with ensembl gene information
         hgnc_lines(iterable(str)): Lines with gene information from genenames.org
         exac_lines(iterable(str)): Lines with information pLi-scores from ExAC
         mim2gene(iterable(str)): Lines with map from omim id to gene symbol
@@ -78,20 +95,36 @@ def load_hgnc_genes(
             genemap_lines=genemap_lines,
         )
 
-    non_existing = 0
+    without_coords = 0
     nr_genes = len(genes)
     LOG.info(f"Building info for {nr_genes} genes")
+
+    cytoband_coords: Dict[str, dict] = adapter.cytoband_to_coordinates(build=build)
+
     with progressbar(genes.values(), label="Building genes", length=nr_genes) as bar:
         for gene_data in bar:
+            set_missing_gene_coordinates(gene_data=gene_data, cytoband_coords=cytoband_coords)
+
             if not gene_data.get("chromosome"):
-                non_existing += 1
+                without_coords += 1
                 continue
+            gene_obj = build_hgnc_gene(
+                gene_data,
+                build=build,
+            )
 
-            gene_obj = build_hgnc_gene(gene_data, build=build)
-            gene_objects.append(gene_obj)
+            if gene_obj:
+                gene_objects.append(gene_obj)
+            else:
+                without_coords += 1
 
-    LOG.info("Nr of genes without coordinates in build %s: %s", build, non_existing)
+    LOG.info(
+        "Nr of genes without coordinates in build %s and therefore skipped: %s",
+        build,
+        without_coords,
+    )
     LOG.info(f"Loading {len(gene_objects)} genes into the database")
+
     adapter.load_hgnc_bulk(gene_objects)
 
     LOG.info("Loading done. %s genes loaded", len(gene_objects))

{scout-browser-4.84 → scout-browser-4.85}/scout/parse/hgnc.py

@@ -24,6 +24,7 @@ def parse_hgnc_line(line, header):
     hgnc_gene["hgnc_symbol"] = hgnc_symbol
     hgnc_gene["hgnc_id"] = int(raw_info["hgnc_id"].split(":")[-1])
     hgnc_gene["description"] = raw_info["name"]
+    hgnc_gene["location"] = raw_info["location"]  # cytoband
 
     # We want to have the current symbol as an alias
     aliases = set([hgnc_symbol, hgnc_symbol.upper()])

{scout-browser-4.84 → scout-browser-4.85}/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-browser-4.84 → scout-browser-4.85}/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-browser-4.84 → scout-browser-4.85}/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 []
     ):
@@ -479,6 +482,18 @@ 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 +525,6 @@ 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-browser-4.84 → scout-browser-4.85}/scout/server/blueprints/cases/templates/cases/case.html

@@ -352,7 +352,7 @@
                   <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 %}

{scout-browser-4.84 → scout-browser-4.85}/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>

{scout-browser-4.84 → scout-browser-4.85}/scout/server/blueprints/cases/templates/cases/gene_panel.html

@@ -9,7 +9,7 @@
         <thead class="table-light thead">
           <tr style="cursor: pointer; white-space: nowrap">
             <th>Panel <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by gene panel name"></i></th>
-            <th >Default <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by default panel"></i></th>
+            <th>Default <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by if panel is default"></i></th>
             <th>Version <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by panel version"></i></th>
             <th>Genes <i class="fas fa-sort" data-bs-toggle="tooltip" title="Sort by number of genes"></i></th>
           </tr>
@@ -20,10 +20,10 @@
               <td>
                 <a {% if panel.is_default %} class="text-white" {% endif %} href="{{ url_for('panels.panel', panel_id=panel.panel_id, case_id=case._id, institute_id=institute._id) }}">
                   {{ panel.display_name|truncate(30, True) }}
-                  {% if panel.removed %}
-                    <span class="badge bg-danger">Removed</span>
-                  {% endif %}
                 </a>
+                {% if panel.removed %}
+                  <span class="badge bg-danger">Removed</span>
+                {% endif %}
               </td>
               <td >
                 {% if panel.is_default %}
@@ -35,53 +35,39 @@
             </tr>
           {% else %}
             <tr>
-              <td colspan="5">No panels linked to case</td>
+              <td colspan="4">No panels linked to case</td>
             </tr>
           {% endfor %}
         </tbody>
       </table>
     </div>
-    <div class="card-body">
-      <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
-        <div class="row">
-          <label>Change default gene panels</label>
-        </div>
-        <div class="row">
-          <div class="col-8">
-            <select name="panel_ids" class="selectpicker" multiple="multiple" data-style="btn-secondary">
-              {% for panel in case.panels %}
-                <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>{{ panel.display_name }}</option>
-              {% endfor %}
-            </select>
-          </div>
-          <div class="col-4">
-            <button class="btn btn-secondary form-control">Save</button>
-          </div>
-        </div>
-      </form>
-    </div>
+    {{ change_default_panels(case, institute) }}
+
   </div>
 {% endmacro %}
 
 {% macro change_default_panels(case, institute) %}
-  <div class="card panel-default">
-    <div class="panel-heading">Change default gene panels</div>
-    <div class="card-body">
-      <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
-        <div class="row">
-          <div class="col-xs-4">
-            <select name="panel_ids" class="form-control" multiple>
-              {% for panel in case.panels %}
-                <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>{{ panel.display_name }}</option>
-              {% endfor %}
-            </select>
-          </div>
-          <div class="col-xs-4">
-            <button class="btn btn-secondary form-control">Save</button>
-          </div>
+  <div class="card-body">
+    <form action="{{ url_for('cases.default_panels', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
+      <div class="row">
+        <label>Change default gene panels</label>
+      </div>
+
+      <div class="row">
+        <div class="col-8">
+          <select name="panel_ids" class="selectpicker" multiple="multiple" data-style="btn-secondary">
+            {% for panel in case.panels|sort(attribute='display_name')  %}
+              <option value="{{ panel.panel_id }}" {% if panel.is_default %} selected {% endif %}>
+                {{ panel.display_name }} {% if panel.removed %} (Removed) {% endif %}
+              </option>
+            {% endfor %}
+          </select>
         </div>
-      </form>
-    </div>
+        <div class="col-4">
+          <button class="btn btn-secondary form-control">Save</button>
+        </div>
+      </div>
+    </form>
   </div>
 {% endmacro %}
 

{scout-browser-4.84 → scout-browser-4.85}/scout/server/blueprints/cases/templates/cases/utils.html

@@ -676,7 +676,7 @@
               name="{{ button_name if button_name }}"
               value="{{ button_value if button_value }}"
               type="submit">
-        <i class="fa fa-remove text-danger""></i>
+        <i class="fa fa-times text-danger"></i>
       </button>
     </div>
   </form>

{scout-browser-4.84 → scout-browser-4.85}/scout/server/templates/utils.html

@@ -145,7 +145,7 @@
                   <span class='badge bg-secondary'>edited</span>
                 {% endif %}
                 {% if comment.user_id == current_user.email %}
-                  <button class="btn btn-link btn-sm" type="submit" name="remove"><i class="fa fa-remove"></i></button>
+                  <button class="btn btn-link btn-sm" type="submit" name="remove"><i class="fa fa-times"></i></button>
                   <button class="btn btn-link btn-sm" type="button" data-bs-toggle="modal" data-bs-target="#editComment_{{index}}"><i class="fa fa-edit"></i></button>
                 {% endif %}
               </small>

{scout-browser-4.84 → scout-browser-4.85/scout_browser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.84
+Version: 4.85
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

{scout-browser-4.84 → scout-browser-4.85}/scout_browser.egg-info/requires.txt

@@ -1,4 +1,4 @@
-werkzeug<3
+werkzeug
 Flask>=2.0
 Flask-Bootstrap
 Flask-CORS

{scout-browser-4.84 → scout-browser-4.85}/tests/build/conftest.py

@@ -31,6 +31,7 @@ def test_gene():
         "chromosome": 1,  # required
         "start": 10,  # required
         "end": 100,  # required
+        "location": "11p3.1",
         "description": "A gene",  # Gene description
         "aliases": ["test"],  # Gene symbol aliases, includes hgnc_symbol, str
         "entrez_id": 1,

{scout-browser-4.84 → scout-browser-4.85}/tests/load/test_load_hgnc_genes.py

@@ -1,6 +1,4 @@
-from pprint import pprint as pp
-
-from scout.load.hgnc_gene import load_hgnc_genes
+from scout.load.hgnc_gene import load_hgnc_genes, set_missing_gene_coordinates
 
 
 def test_load_hgnc_genes(
@@ -65,3 +63,27 @@ def test_load_hgnc_genes_no_omim(
 
     # THEN assert that the last gene was loaded
     assert adapter.hgnc_gene(gene_info["hgnc_id"])
+
+
+def test_set_missing_gene_coordinates():
+    """Test function that sets coordinates for genes without ensembl_gene_id."""
+
+    # GIVEN a gene with blank ensembl_gene_id key:
+    gene_dict = {
+        "hgnc_id": 5477,
+        "hgnc_symbol": "IGH",
+        "ensembl_gene_id": "",
+        "location": "14q32.33",
+    }
+
+    # GIVEN cytoband coordinates containing that specific band:
+    cytoband_coords = {"14q32.33": {"chromosome": "14", "start": 104000001, "stop": 107349541}}
+
+    # THEN the set_gene_coordinates function should set coordinates to the genes:
+    set_missing_gene_coordinates(gene_data=gene_dict, cytoband_coords=cytoband_coords)
+
+    for coord in ["chromosome", "start", "end"]:
+        assert coord in gene_dict
+
+    # THEN Ensembl ID should also be set to None
+    assert gene_dict["ensembl_gene_id"] is None

scout-browser-4.84/scout/__version__.py

@@ -1 +0,0 @@
-__version__ = "4.84"