scout-browser 4.84__py3-none-any.whl → 4.85__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.84"
+__version__ = "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/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/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/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/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/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/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/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/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/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/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/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.dist-info → scout_browser-4.85.dist-info}/METADATA

@@ -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
@@ -15,7 +15,7 @@ Classifier: Topic :: Software Development :: Libraries
 Classifier: Programming Language :: Python :: 3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: werkzeug <3
+Requires-Dist: werkzeug
 Requires-Dist: Flask >=2.0
 Requires-Dist: Flask-Bootstrap
 Requires-Dist: Flask-CORS

{scout_browser-4.84.dist-info → scout_browser-4.85.dist-info}/RECORD

@@ -1,5 +1,5 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=tF83DHOdm3YmXrOU1LzFYhwaXBo2y3-VFlwB8yTrpXw,21
+scout/__version__.py,sha256=0tKXeulzMZX3om2NQDhtJ8c6Oms2h9SN1SxrM5kH4Q4,21
 scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
 scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
 scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
@@ -9,11 +9,11 @@ scout/adapter/mongo/case.py,sha256=wXYmyv32gvnCGHgqys3ZGG3gAUyf_buC8LfSzDt4TFo,5
 scout/adapter/mongo/case_events.py,sha256=slHR4XJF9vRuEbuInJKMMAImLF8m7tHWVfGP42fbXr0,26859
 scout/adapter/mongo/case_group.py,sha256=tG8DuO0rNYepV4k0yCGPqssODErc0HMsAypg3mfhcV0,1575
 scout/adapter/mongo/clinvar.py,sha256=tczC39O3DFDkYgjt2RDgkkG-x1Mvx_99Hw7dAbIQ5gk,19838
-scout/adapter/mongo/cytoband.py,sha256=pOWMvOn7lLATk_ShuzRWnGa3xRyILGRJRxh4VONCw7k,2082
+scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7uQ,2622
 scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
 scout/adapter/mongo/event.py,sha256=NnURFhS5odOXk7So_gGMHmALPAJM0PWzESI4FC06azE,19842
 scout/adapter/mongo/filter.py,sha256=GoPqMDqteE1pDiVfpUP8xxT_1A8s7S4ByITCJGdesok,7570
-scout/adapter/mongo/hgnc.py,sha256=qklk7rKO8TCklh6XvjgWXiB-BZ9Vkp-SFRM1-xgfX1s,16407
+scout/adapter/mongo/hgnc.py,sha256=Zcnf_kKJqrJAf62tUFODhL8OQUb695XnL_rzk4D9nes,16411
 scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
 scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,3577
 scout/adapter/mongo/institute.py,sha256=GQmMKb_VzsvWwadp6gXHlSSpcG5ovF1ozdTzvpTFLpA,7025
@@ -99,7 +99,7 @@ scout/commands/update/base.py,sha256=XxxBGzn9JdFfk39jsZbU5eAZhE41MLq73WwLqa_u4Rc
 scout/commands/update/case.py,sha256=q7gjMS4izlrV0LghfTM9GiJeXI0K4qtmO62TqfTqizw,5822
 scout/commands/update/compounds.py,sha256=vwCtb6045tGovKWHqY_uL8w1l9rZ_Hxlt0gUU0cKXUk,753
 scout/commands/update/disease.py,sha256=AajPLoEtd9YeU3jf7S7ZQRs3_o1H3GSxHsST_sVaIZQ,3846
-scout/commands/update/genes.py,sha256=ngzdPodG9qosQYOMKE9x-rMjniZU3T1d5vmuMrduKJY,7082
+scout/commands/update/genes.py,sha256=GhYIn2zWrAZMhdJjzzrpo8AquFqr7XOvosOk8lg4Zwk,6989
 scout/commands/update/hpo.py,sha256=eyCuUlUwPmyP0oLh1olXhdqInlUXDdLe8ylgTlHWi-g,1339
 scout/commands/update/individual.py,sha256=lwVQcKCZj5VxUSO8CcBUsvVRl3ZHgJVe4AE9pcJS7ys,4007
 scout/commands/update/institute.py,sha256=ms8mmTGfCXqxeh_vSB1cdNDGrdHoSSgh9ryhB5GrJQc,1727
@@ -364,7 +364,7 @@ scout/load/all.py,sha256=F_eb7lWM3wYASEL06qDeNczQTM3QR9Zz76nLgchaN5I,3699
 scout/load/cytoband.py,sha256=vPU8oQm31WMcnaG9QG2le9pe_8g70O1S0q1Ljj3Ce84,1356
 scout/load/disease.py,sha256=eZ-RDTtfO6-YCk0tCHuhCWxw1FSCwHNZEemWXCC4P_w,2747
 scout/load/exon.py,sha256=ONaWJ9EfbhGV8KGXxwlq_jYCoU-JkBpv4r9zDaCjtls,2070
-scout/load/hgnc_gene.py,sha256=9bfelQgx71FTeZpn1-5_-Gww_JqFtz8pqMZN6rSXQys,3444
+scout/load/hgnc_gene.py,sha256=GcSQ01CioYIshAzXAv4msIGDPjTjGBBPBnLX2GvaZJ4,4507
 scout/load/hpo.py,sha256=ZWYjV9j6OfpI-ZZuhTQVEs_xgLa7ST2KuvYLW6ku0PY,2474
 scout/load/institute.py,sha256=etmZ0CZRHOVi3f9R-wn5BK1pZPhtZwq2QYbh2RXXxDc,625
 scout/load/panel.py,sha256=JQqkyUdpvhFnW81n8Sq-iPahDcm1hGBzLfrwUcVqt4k,9446
@@ -399,7 +399,7 @@ scout/parse/cytoband.py,sha256=7flY3b_wegupHHBLRcs4KyM1ns-uzuTfVHm4CycnupE,1055
 scout/parse/disease_terms.py,sha256=-JIm4GWEvqg9nmWehK18mlIQ-N5nZhT2u5pbfDRXoxE,7437
 scout/parse/ensembl.py,sha256=nnqOVtLgWh9wbtHnzGIidnNIvRoOp2bTct5OuAFSSB0,10618
 scout/parse/exac.py,sha256=VbahYYoMl8RkffChAhKnrVOS6fzQdDKRkPMPZnKnZcQ,1972
-scout/parse/hgnc.py,sha256=dSV-gIHv6n1wwPc_zpJpuh7r3o1LZ86JVdRZGmJlewI,3189
+scout/parse/hgnc.py,sha256=92ro9ilOLi96AmlbXLItzDKPjJjgUd8iqzQbsy5AOeo,3250
 scout/parse/hpo_mappings.py,sha256=UJY38iLmpJFnZ9FuRaNIGhNQnTx7_WASxr9mlEnhvHE,2637
 scout/parse/hpo_terms.py,sha256=ZJCKFD0rV3jiCuoI8Gm1WNTiaOSRRoKOhZ1bYnqwY6I,5732
 scout/parse/matchmaker.py,sha256=5e9NCFQ2rKXNCJTW-ThXoEylEPl3H41cCfQzPATQ2QM,9524
@@ -424,8 +424,8 @@ scout/parse/variant/ids.py,sha256=N_2m7Hgdh7asHdWU4k2dMySsutxp16ODRE_OHy_Niwg,26
 scout/parse/variant/managed_variant.py,sha256=qwmi2sPLwGZM5izSsMpvhQ9vfMHREiwiIzjDCuOdqQo,2288
 scout/parse/variant/models.py,sha256=NrqLXu7PxpIQ0NmjGRIEk4vS_y972VPiexLsZCZpOn0,507
 scout/parse/variant/rank_score.py,sha256=ipFxCTsQHMqObUbzLJlDAKUb3_lk_sqEYzH52myZVVk,486
-scout/parse/variant/transcript.py,sha256=h0-IPDj4Th5aNijyhR1jrwnPe_YZx5QVajqn9ttxE98,13340
-scout/parse/variant/variant.py,sha256=hKsE2b97hRuUpE948VHL5WOL81n-_RKpZBdRGOHaV1A,23759
+scout/parse/variant/transcript.py,sha256=0kxaXWrNAvSiU76ZdIl9PQFzUyj6go6u3BnNhnTk8pg,13359
+scout/parse/variant/variant.py,sha256=CTCaE07GqDg52ZhUPLpEOoEYLgr4y1mPtvRvAsxt5IM,24057
 scout/resources/__init__.py,sha256=i9UVG651subgmOZ-Gm-JKPsXBqr5-50QUDfSpbwmwIw,443
 scout/resources/cytoBand_hg19.txt.gz,sha256=pheUD5b9NlVuvwwnbKwDc2FG80Yg70gvPxVXP-Sqd3k,6147
 scout/resources/cytoBand_hg38.txt.gz,sha256=sqSVmvPlktQ-0hTiTapJM-5UgyV6xDoYZuTF0kPuETs,6105
@@ -446,27 +446,27 @@ scout/server/blueprints/alignviewers/templates/alignviewers/utils.html,sha256=ni
 scout/server/blueprints/api/__init__.py,sha256=HR6HjS7ot1K_8Lt5eQdNT154z_FCdHGSigy8r2LpNCI,26
 scout/server/blueprints/api/views.py,sha256=pbl78wfhrm1T8JmiJDYF3BbTbfFrlF-hQRbuv2GWI0s,3729
 scout/server/blueprints/cases/__init__.py,sha256=_c17kPFITFYcIVphF4V9bf0PZBer8bU3rtVWQnljKDU,52
-scout/server/blueprints/cases/controllers.py,sha256=Hc_A59cGCByo-7mMqFuLU21U5eBVAI_ktObhpFC5PeU,54195
+scout/server/blueprints/cases/controllers.py,sha256=lVBZy7udshXltMZtjkQWP-0ypNHOOagi_Tciqq5PMJ8,54666
 scout/server/blueprints/cases/views.py,sha256=ZfuDfkcOiw7PHUr68mowJyYxUb6_gQObR488mhP6l78,42841
 scout/server/blueprints/cases/static/case_images.js,sha256=pb_gG7DNQc-1lADqSII8YvjBwmHyeQWYVtuu2jyrTlU,14997
 scout/server/blueprints/cases/static/case_styles.css,sha256=2Pgc8pFf9DR5HM1sTdAjaRWhjL-bK5bsQnLpH54HZak,541
 scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkke1UHxjiYWY_gBzWcIkGpdJUA,2978
 scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
-scout/server/blueprints/cases/templates/cases/case.html,sha256=ZwB24L9D4YjPRPaI4McQQ2VBx5dQvAFPN_LhFXvhp5w,36561
+scout/server/blueprints/cases/templates/cases/case.html,sha256=3wpGT8Vfoo3xBOVxf0N-SUpFoZwlHSf3K9vrlOxAL08,36560
 scout/server/blueprints/cases/templates/cases/case_bionano.html,sha256=PLoRv7hDJcHwxhi-0hC9fQSZc7V_aUYHBhhQqcn_2G8,5946
 scout/server/blueprints/cases/templates/cases/case_report.html,sha256=1tosH5xEl6CCZ1P6qlR5OKvWbAC5z3ewKL_JGdgPMBM,63635
 scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=SAcElb4kH05mkPdEdaEbed-vbgQQGfxioCoNZsHljDc,4962
 scout/server/blueprints/cases/templates/cases/case_tabular_view.html,sha256=ko-LDUKmIoTazMZ2nFWvPEZsgObU07RwqIkDYFjokoY,4317
 scout/server/blueprints/cases/templates/cases/chanjo2_form.html,sha256=5Wmk7DM8LI3MynqzxeTzAr_EoEBwVVo31djcI5ZlTdo,2164
-scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html,sha256=tU7vorWKg3rdcDCMDyEaIBL5gGcTv8OvmKO9XRoc2mQ,29247
+scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html,sha256=Az8Oq9ldGtT9snzeDxt1xC68Yp7fp4qZ1eDN7Gr9Wf4,29246
 scout/server/blueprints/cases/templates/cases/diseases.html,sha256=ETTQI0Nrl_v86NoX9mFZcvWD-qM1IJoqPmHPWn__Grw,1677
-scout/server/blueprints/cases/templates/cases/gene_panel.html,sha256=fR2fCb5A_dBUTTyI4GfwARtOC6k9LeFunx8flbb6qko,12309
+scout/server/blueprints/cases/templates/cases/gene_panel.html,sha256=lkC_Piqaq-paYr4GUCwQaR8EgGOUXDMoW5sPLDW7yzg,11628
 scout/server/blueprints/cases/templates/cases/index.html,sha256=oUmjFyUvwP4yo21CxcWy-6eepMFI65hpznMEpSEqKfM,1207
 scout/server/blueprints/cases/templates/cases/individuals_table.html,sha256=DXE7gE0f81B5CxCV1e5bqWv27_HS-9-8nc0pcFkMoOg,11497
 scout/server/blueprints/cases/templates/cases/institutes_sidebar.html,sha256=u0oPGHJ0ipZ1LkjHkbwlWfkUWc1h6XH1nh3tkbX17z0,4546
 scout/server/blueprints/cases/templates/cases/matchmaker.html,sha256=1vwGBhM4HgvRMlO1foKBAwV-Wfvfs1MRvzteOETCZeM,13142
 scout/server/blueprints/cases/templates/cases/phenotype.html,sha256=kBHD13SjBUGz0b79cQ2rfgdx3JPyJGDR38kscGZJai0,16120
-scout/server/blueprints/cases/templates/cases/utils.html,sha256=GbcR0LXW5exdlmZa4fpJ81aEtgN505XqOO29LNJsd0A,34914
+scout/server/blueprints/cases/templates/cases/utils.html,sha256=EwMPMGmHPuDRS3J88Ga4ram2y3fzopVs38HjnvZHfyM,34912
 scout/server/blueprints/clinvar/__init__.py,sha256=BV3aH2AbiA2WWrUEMbGd0H9MefFd2eTsRE9ShywbzpI,30
 scout/server/blueprints/clinvar/controllers.py,sha256=TEOdUTVYI-I_lzts0F3M_TFPMkeeweWIUxWug5HUhDw,24059
 scout/server/blueprints/clinvar/form.py,sha256=d0EBJouYsk-kIpGtAr_SfNCyLoBNchfLt25uFR9HxO0,5155
@@ -639,7 +639,7 @@ scout/server/static/robots.txt,sha256=fFX0beQN4x3mzR3evnZjrOUYOTNkezYAwqMowTUpmx
 scout/server/templates/bootstrap_global.html,sha256=6e09Qyn3pc5zbE82Gacyye9qL5cMbrfOebMSjU9rqqA,2894
 scout/server/templates/layout.html,sha256=-uhRxFA89L0gocv8sPLcODUHmWLNuV6xsjB34Zjq-8o,4635
 scout/server/templates/report_base.html,sha256=PZOqFZRLtbe4PZ7lkVc9LP1O-yh7v3_EzOohRE9Ix4U,1252
-scout/server/templates/utils.html,sha256=9o3zXyAaIcZFmmg1ltYyNk7ow7CYlnf4NbHfeLnp5fg,12941
+scout/server/templates/utils.html,sha256=aFxvkFYA_4S-LBkMGXFWbycLNFZ6QqtO1088bru3i9Y,12940
 scout/server/translations/sv/LC_MESSAGES/messages.mo,sha256=eI53pCtlYj1MXduDicMZRxBhgOV_TlmMUpH7IhncgDY,4452
 scout/server/translations/sv/LC_MESSAGES/messages.po,sha256=Wp7Mx4LoiFNtzsV1tpAoWjMxYnq8SpfpU9a4XWJ7L6g,4531
 scout/update/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -661,9 +661,9 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=JjHOJW1XmenG05mNQ33kvOKq_IicveIfQMcPZeRcQdo,12856
 scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
 scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
-scout_browser-4.84.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.84.dist-info/METADATA,sha256=4IpwKNOjBxH-Kyj_hLJL1mSHA8ZcmKZjERVJ0uIkLG0,14263
-scout_browser-4.84.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-scout_browser-4.84.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.84.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.84.dist-info/RECORD,,
+scout_browser-4.85.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.85.dist-info/METADATA,sha256=-rqJW4SQ9_0iU08QcC2w8nFzgK57yYUDkafy1fBNxHQ,14260
+scout_browser-4.85.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+scout_browser-4.85.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.85.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
+scout_browser-4.85.dist-info/RECORD,,