scout-browser 4.95.0__py3-none-any.whl → 4.97.0__py3-none-any.whl

scout/server/extensions/matchmaker_extension.py

@@ -1,5 +1,5 @@
 """Code for MatchMaker Exchange integration
-   Tested with PatientMatcher: https://github.com/Clinical-Genomics/patientMatcher
+Tested with PatientMatcher: https://github.com/Clinical-Genomics/patientMatcher
 """
 
 import datetime

scout/server/links.py

@@ -3,7 +3,6 @@ from urllib.parse import quote
 
 from flask import current_app
 
-from scout.constants import SPIDEX_HUMAN
 from scout.utils.convert import amino_acid_residue_change_3_to_1
 
 SHALLOW_REFERENCE_STR_LOCI = ["ARX", "HOXA13"]
@@ -486,7 +485,6 @@ def get_variant_links(institute_obj: dict, variant_obj: dict, build: int = None)
         ensembl_link=ensembl_link(variant_obj, build),
         mitomap_link=mitomap_link(variant_obj),
         hmtvar_link=hmtvar_link(variant_obj),
-        spidex_human=spidex_human(variant_obj),
         spliceai_link=spliceai_link(variant_obj, build),
         str_source_link=str_source_link(variant_obj),
         snp_links=snp_links(variant_obj),
@@ -908,18 +906,6 @@ def hmtvar_link(variant_obj):
     return url_template.format(id=variant_obj.get("hmtvar_variant_id"))
 
 
-def spidex_human(variant_obj):
-    """Translate SPIDEX annotation to human readable string."""
-    if variant_obj.get("spidex") is None:
-        return "not_reported"
-    if abs(variant_obj["spidex"]) < SPIDEX_HUMAN["low"]["pos"][1]:
-        return "low"
-    if abs(variant_obj["spidex"]) < SPIDEX_HUMAN["medium"]["pos"][1]:
-        return "medium"
-
-    return "high"
-
-
 def external_primer_order_link(variant_obj, build=None):
     """Compose link for primers orders based on the configuration paramaters EXTERNAL_PRIMER_ORDER_LINK_(37|38)"""
     build = build or 37

scout/server/static/bs_styles.css

@@ -269,6 +269,8 @@ li.nav-item {
 
 /* Introduce small space in between list elements */
 body {
+	min-width: 1000px;
+ 	overflow-x: scroll;
 	background-color: var(--bg-color);
 	font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
 }

scout/server/templates/layout.html

@@ -43,6 +43,7 @@
                 <div class="dropdown-divider" ></div>
                 <a class="dropdown-item" href="https://clinical-genomics.github.io/scout" referrerpolicy="no-referrer" rel="noopener" target='_blank'>User guide</a>
                 <a class="dropdown-item" href="https://github.com/Clinical-Genomics/scout/issues" referrerpolicy="no-referrer" rel="noopener" target='_blank'>Open issues</a>
+                <a class="dropdown-item mb-1" href="https://github.com/Clinical-Genomics/scout/releases/tag/v{{ SCOUT_VERSION[:-2] if SCOUT_VERSION.endswith('.0') and SCOUT_VERSION.count('.') > 1 else SCOUT_VERSION }}" referrerpolicy="no-referrer" rel="noopener" target='_blank'>Release notes v{{SCOUT_VERSION}}</a>
               </div>
             </li>
             {% block top_nav %}{% endblock %}

scout/server/utils.py

@@ -330,6 +330,11 @@ def case_append_alignments(case_obj: dict):
         # Add sample name
         sample_name = f"{case_obj.get('display_name', '')} - {individual.get('display_name', '')}"
         append_safe(case_obj, "sample_names", sample_name)
+        append_safe(
+            case_obj,
+            "track_items_soft_clips_settings",
+            individual.get("analysis_type", "") not in ["wes", "panel"],
+        )
 
         # Process all file settings
         for setting in unwrap_settings:

scout/utils/acmg.py

@@ -1,6 +1,6 @@
 # coding=UTF-8
 
-from typing import Optional
+from typing import List, Optional
 
 from scout.constants import ACMG_COMPLETE_MAP
 from scout.constants.acmg import ACMG_POTENTIAL_CONFLICTS
@@ -362,12 +362,12 @@ def get_acmg_temperature(acmg_terms: set) -> Optional[dict]:
     }
 
 
-def get_acmg_conflicts(acmg_terms: set) -> list:
-    """Check potential conflict paris, return list of reference strings."""
+def get_acmg_conflicts(acmg_terms: List[str]) -> List[str]:
+    """Check for potential conflicting terms, return a list of references as strings."""
 
     conflicts = []
-    for t1, t2, reference in ACMG_POTENTIAL_CONFLICTS:
-        if t1 in acmg_terms and t2 in acmg_terms:
+    for conflict_set, reference in ACMG_POTENTIAL_CONFLICTS:
+        if conflict_set.issubset(set(acmg_terms)):
             conflicts.append(reference)
 
     return conflicts

scout/utils/ensembl_biomart_clients.py

@@ -4,7 +4,7 @@ from typing import Dict, Iterator
 import requests
 
 LOG = logging.getLogger(__name__)
-SCHUG_BASE = "https://schug.scilifelab.se"
+SCHUG_BASE = "https://schug-stage.scilifelab.se"
 
 BUILDS: Dict[str, str] = {"37": "GRCh37", "38": "GRCh38"}
 
@@ -29,15 +29,6 @@ class EnsemblBiomartHandler:
     def stream_resource(self, interval_type: str) -> Iterator[str]:
         """Use schug web to fetch genes, transcripts or exons from a remote Ensembl biomart in the right genome build and save them to file."""
 
-        def yield_resource_lines(iterable) -> str:
-            """Removes the last element from an iterator."""
-            it = iter(iterable)
-            current = next(it)
-            for i in it:
-                yield current
-                current = i
-
         shug_url: str = f"{SCHUG_BASE}{SCHUG_RESOURCE_URL[interval_type]}{self.build}"
 
-        # return all lines except the last, which contains the "[success]" string
-        return yield_resource_lines(self.stream_get(shug_url))
+        return self.stream_get(shug_url)

scout/utils/scout_requests.py

@@ -324,7 +324,7 @@ def fetch_constraint():
     Returns:
         exac_lines(iterable(str))
     """
-    path = "/release/v4.0/constraint/gnomad.v4.0.constraint_metrics.tsv"
+    path = "/release/4.1/constraint/gnomad.v4.1.constraint_metrics.tsv"
     mirror_urls = [
         f"https://storage.googleapis.com/gcp-public-data--gnomad{path}",
         f"https://gnomad-public-us-east-1.s3.amazonaws.com{path}",

{scout_browser-4.95.0.dist-info → scout_browser-4.97.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.95.0
+Version: 4.97.0
 Summary: Clinical DNA variant visualizer and browser
 Project-URL: Repository, https://github.com/Clinical-Genomics/scout
 Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md