scout-browser 4.89.1__tar.gz → 4.90__tar.gz

{scout-browser-4.89.1 → scout-browser-4.90}/CHANGELOG.md

@@ -4,6 +4,41 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.90]
+### Added
+- Link to chanjo2 MANE coverage overview on case page and panel page
+- More SVI recommendation links on the ACMG page
+- IGV buttons for SMN CN page
+- Warnings on ACMG classifications for potentially conflicting classification pairs
+- ACMG Bayesian foundation point scale after Tavtigian for variant heat profile
+### Changed
+- Variants query backend allows rank_score filtering
+- Added script to tabulate causatives clinical filter rank
+- Do not display inheritance models associated to ORPHA terms on variant page
+- Moved edit and delete buttons close to gene names on gene panel page and other aesthetical fixes
+- SNV VariantS page functional annotation and region annotation columns merged
+- VariantS pages (not cancer) gene cells show OMIM inheritance pattern badges also without hover
+- STR variantS page to show STR inheritance model without hover (fallback to OMIM for non-Stranger annotation)
+- VariantS page local observation badges have counts visible also without hover
+- On Matchmaker page, show number of matches together with matching attempt date
+- Display all custom inheritance models, both standard and non-standard, as gathered from the gene panel information on the variant page
+### Fixed
+- Make BA1 fully stand-alone to Benign prediction
+- Modifying Benign terms to "Moderate" has no effect under Richards. Ignored completely before, will retain unmodified significance now
+- Extract all fields correctly when exporting a panel to file from gene panel page
+- Custom updates to a gene in a panel
+- Gene panel PDF export, including gene links
+- Cancer SV, Fusion, MEI and Outlier filters are shown on the Institute Filters overview
+- CaseS advanced search limit
+- Visibility of Matchmaker Exchange matches on dark mode
+- When creating a new gene panel from file, all gene fields are saved, including comments and manual inheritance models
+- Downloading on gene names from EBI
+- Links to gene panels on variant page, summary panel
+- Exporting gene variants when one or more variants' genes are missing HGNC symbol
+
+## [4.89.2]
+## Fixed
+- If OMIM gene panel gene symbols are not mapping to hgnc_id, allow fallback use of a unique gene alias
 
 ## [4.89.1]
 ### Fixed
@@ -21,6 +56,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Advanced cases search to narrow down results using more than one search parameter
 - Coverage report available for any case with samples containing d4 files, even if case has no associated gene panels
 - RNA delivery reports
+- Two new LRS SV callers (hificnv, severus)
 ### Changed
 - Documentation for OMICS variants and updating a case
 - Include both creation and deletion dates in gene panels pages
@@ -42,6 +78,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Code creating Alamut links for variant genes without canonical_transcript set
 - Variant delete button in ClinVar submissions page
 - Broken search cases by case similarity
+- Missing caller tag for TRGT
 
 ## [4.88.1]
 ### Fixed

{scout-browser-4.89.1/scout_browser.egg-info → scout-browser-4.90}/PKG-INFO

@@ -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

scout-browser-4.90/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.90"

{scout-browser-4.89.1 → scout-browser-4.90}/scout/adapter/mongo/hgnc.py

@@ -335,7 +335,7 @@ class GeneHandler(object):
         Returns:
             alias_genes(dict): {<hgnc_alias>: {'true': <hgnc_id>, 'ids': {<hgnc_id_1>, <hgnc_id_2>, ...}}}
         """
-        LOG.debug("Fetching all genes by alias")
+
         # Collect one entry for each alias symbol that exists
         alias_genes = {}
 

{scout-browser-4.89.1 → scout-browser-4.90}/scout/adapter/mongo/panel.py

@@ -11,6 +11,7 @@ from bson import ObjectId
 from bson.errors import InvalidId
 
 from scout.build import build_panel
+from scout.constants.panels import EXPORT_PANEL_FIELDS
 from scout.exceptions import IntegrityError
 from scout.parse.panel import get_omim_panel_genes
 from scout.utils.date import get_date
@@ -245,8 +246,6 @@ class PanelHandler:
         for panel in res:
             return panel
 
-        LOG.warning("Gene panel not found")
-
         return None
 
     def gene_panels(self, panel_id=None, institute_id=None, version=None, include_hidden=False):
@@ -464,89 +463,53 @@ class PanelHandler:
         )
         return updated_panel
 
-    def apply_pending(self, panel_obj, version):
+    def apply_pending(self, panel_obj: dict, version: float) -> str:
         """Apply the pending changes to an existing gene panel or create a new version of the same panel.
 
-        Args:
-            panel_obj(dict): panel in database to update
-            version(double): panel version to update
-
         Returns:
             inserted_id(str): id of updated panel or the new one
         """
 
-        updates = {}
         new_panel = deepcopy(panel_obj)
         new_panel["pending"] = []
         new_panel["date"] = dt.datetime.now()
-        info_fields = [
-            "disease_associated_transcripts",
-            "inheritance_models",
-            "custom_inheritance_models",
-            "reduced_penetrance",
-            "mosaicism",
-            "database_entry_version",
-            "comment",
-        ]
         new_genes = []
 
-        for update in panel_obj.get("pending", []):
-            hgnc_id = update["hgnc_id"]
-
-            # If action is add we create a new gene object
-            if update["action"] != "add":
-                updates[hgnc_id] = update
-                continue
-            info = update.get("info", {})
-            gene_obj = {"hgnc_id": hgnc_id, "symbol": update["symbol"]}
-
-            for field in info_fields:
-                if field in info:
-                    gene_obj[field] = info[field]
-            new_genes.append(gene_obj)
+        # Process 'add' actions and gather updates
+        updates = {u["hgnc_id"]: u for u in panel_obj.get("pending", []) if u["action"] != "add"}
+        new_genes += [
+            {"hgnc_id": u["hgnc_id"], "symbol": u["symbol"], **u.get("info", {})}
+            for u in panel_obj.get("pending", [])
+            if u["action"] == "add"
+        ]
 
+        # Process existing genes
         for gene in panel_obj.get("genes", []):
             hgnc_id = gene["hgnc_id"]
+            update = updates.get(hgnc_id)
 
-            if hgnc_id not in updates:
+            if not update:  # No update, keep the gene
                 new_genes.append(gene)
-                continue
-
-            current_update = updates[hgnc_id]
-            action = current_update["action"]
-            info = current_update["info"]
-
-            # If action is delete we do not add the gene to new genes
-            if action == "delete":
-                continue
-
-            if action == "edit":
-                for field in info_fields:
-                    if field in info:
-                        gene[field] = info[field]
+            elif update["action"] == "edit":  # Edit gene fields
+                for key in EXPORT_PANEL_FIELDS[2:]:
+                    gene.pop(key[1], None)  # Reset all fields except hgnc and symbol
+                gene.update(update["info"])
                 new_genes.append(gene)
+            # Skip 'delete' actions
 
         new_panel["genes"] = new_genes
         new_panel["version"] = float(version)
 
-        inserted_id = None
-        # if the same version of the panel should be updated
-        if new_panel["version"] == panel_obj["version"]:
-            # replace panel_obj with new_panel
+        # Update same version or create new version
+        if version == panel_obj["version"]:
             result = self.panel_collection.find_one_and_replace(
-                {"_id": panel_obj["_id"]},
-                new_panel,
-                return_document=pymongo.ReturnDocument.AFTER,
+                {"_id": panel_obj["_id"]}, new_panel, return_document=pymongo.ReturnDocument.AFTER
             )
             inserted_id = result["_id"]
-        else:  # create a new version of the same panel
+        else:
             new_panel.pop("_id")
-
-            # archive the old panel
             panel_obj["is_archived"] = True
             self.update_panel(panel_obj=panel_obj, date_obj=panel_obj["date"])
-
-            # insert the new panel
             inserted_id = self.panel_collection.insert_one(new_panel).inserted_id
 
         return inserted_id

{scout-browser-4.89.1 → scout-browser-4.90}/scout/adapter/mongo/query.py

@@ -691,6 +691,15 @@ class QueryHandler(object):
 
                 mongo_secondary_query.append(revel_query)
 
+            if criterion == "rank_score":
+                rank_score_query = {
+                    "$or": [
+                        {"rank_score": {"$gte": float(query["rank_score"])}},
+                        {"rank_score": {"$exists": False}},
+                    ]
+                }
+                mongo_secondary_query.append(rank_score_query)
+
             if criterion == "cadd_score":
                 cadd = query["cadd_score"]
                 cadd_query = {"cadd_score": {"$gt": float(cadd)}}

{scout-browser-4.89.1 → scout-browser-4.90}/scout/build/panel.py

@@ -1,94 +1,58 @@
 # -*- coding: utf-8 -*-
 import logging
-from datetime import datetime as datetime
 
-from scout.constants import VALID_MODELS
 from scout.exceptions import IntegrityError
 
 LOG = logging.getLogger(__name__)
 
 
-def build_gene(gene_info, adapter):
-    """Build a panel_gene object
+def build_gene(gene_info: dict, adapter) -> dict:
+    """Build a panel_gene object."""
 
-    Args:
-        gene_info(dict)
-
-    Returns:
-        gene_obj(dict)
-
-        panel_gene = dict(
-            hgnc_id = int, # required
-            symbol = str,
-
-            disease_associated_transcripts = list, # list of strings that represent refseq transcripts
-            reduced_penetrance = bool,
-            mosaicism = bool,
-            database_entry_version = str,
-            comment = str, # panel level gene comment str
-
-            ar = bool,
-            ad = bool,
-            mt = bool,
-            xr = bool,
-            xd = bool,
-            x = bool,
-            y = bool,
-        )
-
-    """
     symbol = gene_info.get("hgnc_symbol")
-    try:
-        # A gene has to have a hgnc id
-        hgnc_id = gene_info["hgnc_id"]
-        if not hgnc_id:
-            raise KeyError()
-    except KeyError as err:
-        raise KeyError(
-            "Gene {0} is missing hgnc id. Panel genes has to have hgnc_id".format(symbol)
-        )
+    hgnc_id = gene_info.get("hgnc_id")
+
+    # Validate presence of hgnc_id
+    if not hgnc_id:
+        raise KeyError(f"Gene {symbol} is missing hgnc id. Panel genes must have hgnc_id.")
 
+    # Try fetching gene information from either build "37" or "38"
     hgnc_gene = adapter.hgnc_gene_caption(
         hgnc_identifier=hgnc_id, build="37"
     ) or adapter.hgnc_gene_caption(hgnc_identifier=hgnc_id, build="38")
+
     if hgnc_gene is None:
-        raise IntegrityError("hgnc_id {0} is not in the gene database!".format(hgnc_id))
+        raise IntegrityError(f"hgnc_id {hgnc_id} is not in the gene database!")
 
-    gene_obj = dict(hgnc_id=hgnc_id)
+    gene_obj = {"hgnc_id": hgnc_id, "symbol": hgnc_gene["hgnc_symbol"]}
 
-    gene_obj["symbol"] = hgnc_gene["hgnc_symbol"]
+    # Log warnings if symbols do not match
     if symbol != gene_obj["symbol"]:
-        LOG.warning(
-            "Symbol in database does not correspond to symbol in panel file for gene %s",
-            hgnc_id,
-        )
-        LOG.warning(
-            "Using symbol %s for gene %s, instead of %s"
-            % (hgnc_gene["hgnc_symbol"], hgnc_id, symbol)
-        )
+        LOG.warning(f"Symbol in database does not match symbol in panel file for gene {hgnc_id}")
+        LOG.warning(f"Using symbol {gene_obj['symbol']} for gene {hgnc_id} instead of {symbol}")
+
+    # Add optional gene information
+    gene_obj.update(
+        {
+            key: gene_info[key]
+            for key in ["disease_associated_transcripts", "comment", "database_entry_version"]
+            if key in gene_info
+        }
+    )
+
+    # Add boolean flags
+    gene_obj.update(
+        {key: True for key in ["reduced_penetrance", "mosaicism"] if gene_info.get(key)}
+    )
+
+    # Handle inheritance models
+    if "inheritance_models" in gene_info:
+        gene_obj["inheritance_models"] = gene_info["inheritance_models"]
 
-    if gene_info.get("transcripts"):
-        gene_obj["disease_associated_transcripts"] = gene_info["transcripts"]
-
-    for gene_member_variable_str in ["comment", "database_entry_version"]:
-        if gene_info.get(gene_member_variable_str):
-            gene_obj[gene_member_variable_str] = gene_info[gene_member_variable_str]
-
-    for gene_member_variable_bool in ["reduced_penetrance", "mosaicism"]:
-        if gene_info.get(gene_member_variable_bool):
-            gene_obj[gene_member_variable_bool] = True
-
-    if gene_info.get("inheritance_models"):
-        gene_obj["inheritance_models"] = []
-        custom_models = []
-        for model in gene_info["inheritance_models"]:
-            if model not in VALID_MODELS:
-                custom_models.append(model)
-                continue
-            gene_obj["inheritance_models"].append(model)
-            lc_model = model.lower()  # example ad = True
-            gene_obj[lc_model] = True
-        gene_obj["custom_inheritance_models"] = custom_models
+    if "custom_inheritance_models" in gene_info:
+        gene_obj["custom_inheritance_models"] = [
+            model for model in gene_info["custom_inheritance_models"]
+        ]
 
     return gene_obj
 

{scout-browser-4.89.1 → scout-browser-4.90}/scout/constants/__init__.py

@@ -64,7 +64,6 @@ from .gene_tags import (
     PANEL_GENE_INFO_TRANSCRIPTS,
     PANELAPP_CONFIDENCE_EXCLUDE,
     UPDATE_GENES_RESOURCES,
-    VALID_MODELS,
 )
 from .igv_tracks import CASE_SPECIFIC_TRACKS, HUMAN_REFERENCE, IGV_TRACKS, USER_DEFAULT_TRACKS
 from .indexes import ID_PROJECTION, INDEXES
@@ -79,6 +78,7 @@ from .phenotype import (
 from .query_terms import FUNDAMENTAL_CRITERIA, PRIMARY_CRITERIA, SECONDARY_CRITERIA
 from .so_terms import SEVERE_SO_TERMS, SEVERE_SO_TERMS_SV, SO_TERM_KEYS, SO_TERMS
 from .variant_tags import (
+    CALLERS,
     CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
     CANCER_TIER_OPTIONS,
     CONSEQUENCE,
@@ -145,6 +145,33 @@ CHROMOSOMES_38 = AUTOSOMES + ["X", "Y", "M"]
 # Maps chromosomes to integers
 CHROMOSOME_INTEGERS = {chrom: i + 1 for i, chrom in enumerate(CHROMOSOMES)}
 
+GENOME_REGION = {
+    "37": {
+        "smn1": {
+            "chrom": 5,
+            "start": 70247713,
+            "end": 70247832,
+        },
+        "smn2": {
+            "chrom": 5,
+            "start": 69372279,
+            "end": 69372427,
+        },
+    },
+    "38": {
+        "smn1": {
+            "chrom": 5,
+            "start": 70951877,
+            "end": 70952014,
+        },
+        "smn2": {
+            "chrom": 5,
+            "start": 70076451,
+            "end": 70076603,
+        },
+    },
+}
+
 
 PAR_COORDINATES = {
     "37": {
@@ -181,50 +208,6 @@ PAR_COORDINATES = {
     },
 }
 
-CALLERS = {
-    "snv": [
-        {"id": "gatk", "name": "GATK"},
-        {"id": "freebayes", "name": "Freebayes"},
-        {"id": "samtools", "name": "SAMtools"},
-        {"id": "bcftools", "name": "Bcftools"},
-        {"id": "deepvariant", "name": "DeepVariant"},
-    ],
-    "cancer": [
-        {"id": "mutect", "name": "MuTect"},
-        {"id": "pindel", "name": "Pindel"},
-        {"id": "gatk", "name": "GATK"},
-        {"id": "freebayes", "name": "Freebayes"},
-        {"id": "tnscope", "name": "TNScope"},
-        {"id": "tnscope_umi", "name": "TNscope_UMI"},
-        {"id": "vardict", "name": "VarDict"},
-    ],
-    "cancer_sv": [
-        {"id": "gatk", "name": "GATK"},
-        {"id": "manta", "name": "Manta"},
-        {"id": "dellysv", "name": "DellySV"},
-        {"id": "cnvkit", "name": "CNVkit"},
-        {"id": "ascat", "name": "ASCAT"},
-        {"id": "dellycnv", "name": "DellyCNV"},
-        {"id": "tiddit", "name": "TIDDIT"},
-        {"id": "igh_dux4", "name": "IGH-DUX4 detection"},
-    ],
-    "mei": [{"id": "retroseq", "name": "RetroSeq"}],
-    "sv": [
-        {"id": "gatk", "name": "GATK"},
-        {"id": "cnvnator", "name": "CNVnator"},
-        {"id": "cnvpytor", "name": "CNVpytor"},
-        {"id": "delly", "name": "Delly"},
-        {"id": "sniffles", "name": "Sniffles"},
-        {"id": "tiddit", "name": "TIDDIT"},
-        {"id": "manta", "name": "Manta"},
-    ],
-    "str": [{"id": "expansionhunter", "name": "ExpansionHunter"}],
-    "fusion": [
-        {"id": "arriba", "name": "Arriba"},
-        {"id": "starfusion", "name": "STARfusion"},
-        {"id": "fusioncatcher", "name": "FusionCatcher"},
-    ],
-}
 
 BND_ALT_PATTERN = re.compile(r".*[\],\[](.*?):(.*?)[\],\[]")
 CHR_PATTERN = re.compile(r"(chr)?(.*)", re.IGNORECASE)