scout-browser 4.87__tar.gz → 4.88__tar.gz

{scout-browser-4.87 → scout-browser-4.88}/CHANGELOG.md

@@ -4,6 +4,23 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.88]
+### Added
+- Added CoLoRSdb frequency to Pop Freq column on variantS page
+- Hovertip to gene panel names with associated genes in SV variant view, when variant covers more than one gene
+- RNA sample ID can be provided in case load config if different from sample_id
+### Fixed
+- Broken `scout setup database` command
+- Update demo VCF header, adding missing keys found on variants
+- Broken upload to Codecov step in Tests & Coverage GitHub action
+- Tomte DROP column names have been updated (backwards compatibility preserved for main fields)
+- WTS outlierS view to display correct individual IDs for cases with multiple individuals
+- WTS outlierS not displayed on WTS outlierS view
+
+## [4.87.1]
+### Fixed
+- Positioning and alignment of genes cell on variantS page
+
 ## [4.87]
 ### Added
 - Option to configure RNA build on case load (default '38')

{scout-browser-4.87/scout_browser.egg-info → scout-browser-4.88}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.87
+Version: 4.88
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.88/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.88"

{scout-browser-4.87 → scout-browser-4.88}/scout/adapter/mongo/case.py

@@ -534,6 +534,8 @@ class CaseHandler(object):
                 {"RNAfusion_report_research": EXISTS_NOT_NULL},
                 {"RNAfusion_inspector": EXISTS_NOT_NULL},
                 {"RNAfusion_inspector_research": EXISTS_NOT_NULL},
+                {"omics_files.fraser": EXISTS_NOT_NULL},
+                {"omics_files.outrider": EXISTS_NOT_NULL},
             ],
         }
         return [case["_id"] for case in self.case_collection.find(query)]

{scout-browser-4.87 → scout-browser-4.88}/scout/adapter/mongo/omics_variant.py

@@ -33,20 +33,60 @@ class OmicsVariantHandler:
 
         LOG.info("%s variants deleted", result.deleted_count)
 
+    def get_matching_omics_sample_id(self, case_obj: dict, omics_model: dict) -> dict:
+        """Select individual that matches omics model sample on omics_sample_id if these are provided."""
+        for ind in case_obj.get("individuals"):
+            if omics_model["sample_id"] == ind.get("omics_sample_id"):
+                return ind
+
+    def get_matching_sample_id(self, case_obj: dict, omics_model: dict) -> dict:
+        """
+        Select individual that matches omics model on sample id (as when we are loading a pure RNA case eg).
+        """
+        for ind in case_obj.get("individuals"):
+            if omics_model["sample_id"] == ind.get("individual_id"):
+                return ind
+
+    def _get_affected_individual(self, case_obj: dict) -> dict:
+        """
+        Fall back to assigning the variants to an individual with affected status to have them display
+        on variantS queries.
+        """
+        for ind in case_obj.get("individuals"):
+            if ind.get("phenotype") in [2, "affected"]:
+                return ind
+
+    def _get_first_individual(self, case_obj: dict) -> dict:
+        """
+        Fall back to assigning the variants to any one individual to have them display
+        on variantS queries.
+        """
+        return case_obj.get("individuals")[0]
+
     def set_samples(self, case_obj: dict, omics_model: dict):
-        """Internal member function to connect individuals.
-        OMICS variants do not have a genotype as such."""
+        """Internal member function to connect individuals for a single OMICS variant.
+        OMICS variants do not have a genotype as such.
+        Select individuals that match on omics_sample_id if these are provided.
+        For a fallback, match on sample id (as when we are loading a pure RNA case eg),
+        or fall back to assigning the variants to an individual with affected status to have them display
+        on variantS queries.
+        ."""
 
         samples = []
 
-        for ind in case_obj.get("individuals"):
-            if omics_model["sampleID"] == ind.get("individual_id"):
-                sample = {
-                    "sample_id": ind["individual_id"],
-                    "display_name": ind["display_name"],
-                    "genotype_call": "./1",
-                }
-                samples.append(sample)
+        match = (
+            self.get_matching_omics_sample_id(case_obj, omics_model)
+            or self.get_matching_sample_id(case_obj, omics_model)
+            or self._get_affected_individual(case_obj)
+            or self._get_first_individual(case_obj)
+        )
+
+        sample = {
+            "sample_id": match["individual_id"],
+            "display_name": match["display_name"],
+            "genotype_call": "./1",
+        }
+        samples.append(sample)
 
         omics_model["samples"] = samples
 

{scout-browser-4.87 → scout-browser-4.88}/scout/build/individual.py

@@ -142,4 +142,8 @@ def build_individual(ind: dict) -> dict:
     ind_obj["bionano_access"] = ind.get("bionano_access", None)
     ind_obj["fshd_loci"] = ind.get("fshd_loci", None)
 
+    # omics variants
+    if "omics_sample_id" in ind:
+        ind_obj["omics_sample_id"] = ind["omics_sample_id"]
+
     return ind_obj

{scout-browser-4.87 → scout-browser-4.88}/scout/build/variant/gene.py

@@ -54,7 +54,8 @@ def build_gene(gene, hgncid_to_gene=None):
     if hgnc_gene:
         # Set the hgnc symbol etc to the one internally in Scout
         gene_obj["hgnc_symbol"] = hgnc_gene["hgnc_symbol"]
-        gene_obj["ensembl_id"] = hgnc_gene["ensembl_id"]
+        if "ensembl_id" in hgnc_gene:
+            gene_obj["ensembl_id"] = hgnc_gene["ensembl_id"]
         gene_obj["description"] = hgnc_gene["description"]
 
         if hgnc_gene.get("inheritance_models"):

{scout-browser-4.87 → scout-browser-4.88}/scout/commands/update/individual.py

@@ -25,6 +25,7 @@ UPDATE_DICT = {
     "rhocall_wig": "path",
     "rna_alignment_path": "path",
     "rna_coverage_bigwig": "path",  # Coverage islands generated from bam or cram files (RNA-seq analysis)
+    "omics_sample_id": "str",  # RNA sample id for connected wts outliers
     "splice_junctions_bed": "path",  # An indexed junctions .bed.gz file obtained from STAR v2 aligner *.SJ.out.tab file.
     "subject_id": "str",  # Individual subject_id (for matching multiomics data and statistics)
     "tiddit_coverage_wig": "path",

{scout-browser-4.87 → scout-browser-4.88}/scout/demo/643594.config.yaml

@@ -40,6 +40,7 @@ samples:
         'alignment_index': 'scout/demo/REViewer_test_data/justhusky_exphun_hugelymodelbat_realigned.bam.bai'
         'vcf': 'scout/demo/REViewer_test_data/justhusky_exphun_hugelymodelbat.vcf'
         'catalog': 'scout/demo/REViewer_test_data/catalog_test.json'
+    omics_sample_id: RNA1059A2
     rna_alignment_path: scout/demo/reduced_mt.bam
     rna_coverage_bigwig: scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered.bigWig
     splice_junctions_bed: scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered_sorted.bed.gz
@@ -62,6 +63,7 @@ samples:
     mitodel_file: scout/demo/mitodel_test_files/slowlycivilbuck_lanes_1_sorted_md_mitodel.txt
     mt_bam: scout/demo/reduced_mt.bam
     vcf2cytosure: scout/demo/ADM1059A1.test.cgh
+    omics_sample_id: RNA1059A1
     rna_alignment_path: scout/demo/reduced_mt.bam
     rna_coverage_bigwig: scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered.bigWig
     splice_junctions_bed: scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered_sorted.bed.gz
@@ -80,6 +82,7 @@ samples:
     mitodel_file: scout/demo/mitodel_test_files/earlycasualcaiman_lanes_1_sorted_md_mitodel.txt
     mt_bam: scout/demo/reduced_mt.bam
     vcf2cytosure: scout/demo/ADM1059A3.test.cgh
+    omics_sample_id: RNA1059A3
     rna_alignment_path: scout/demo/reduced_mt.bam
     rna_coverage_bigwig: scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered.bigWig
     splice_junctions_bed: scout/demo/ACC5963A1_lanes_1234_star_sorted_sj_filtered_sorted.bed.gz

scout-browser-4.88/scout/demo/drop/fraser_top_hits_clinical.tsv

@@ -0,0 +1,5 @@
+hgncId	geneID	hgncSymbol	geneType	geneNameOrig	sampleID	seqnames	start	end	width	strand	type	pValue	psiValue	deltaPsi	counts	totalCounts	meanCounts	meanTotalCounts	nonsplitCounts	nonsplitProportion	nonsplitproportion99quantile	annotatedJunction	pValueGene	padjustGene	pairedEnd	dnaId	dropGroup	spliceCountsDir	hpoTerms	geneCountsFile	geneAnnotation	genome	isExternal	potentialImpact	causesFrameshift	utrOverlap	blacklist
+2439	ENSG00000119535.18	CSF3R	protein_coding	CSF3R	RNA1059A2	chr1	36479517	Imp	1961	-	jaccard	1.6652e-06	0.49	-0.39	127	258	4237.77	4570.55	3	0.01	0.02	both	9.9912e-06		True		outrider,fraser						False	annotatedIntron_reducedUsage	unlikely	5'-UTR	False
+4831	ENSG00000213934.9	HBG1	protein_coding	HBG1	RNA1059A2	chr11	5248488	5254291	5804	-	jaccard	1.918e-12	0.36	0.35	35	96	22.84	6902.91	0	0.0	0.0	end	5.7541e-12	1.2885e-08	True		outrider,fraser						False	exonSkipping	inconclusive	3'-UTR	False
+4832	ENSG00000196565.15	HBG2	protein_coding	HBG2	RNA1059A2	chr11	5248488	5254291	5804	-	jaccard	1.918e-12	0.36	0.35	35	96	22.84	6902.91	0	0.0	0.0	end	3.836e-12	1.2885e-08	True		outrider,fraser						False	exonSkipping	inconclusive	3'-UTR	False
+17284	ENSG00000213934.9	POT1	protein_coding	POT1	RNA1059A2	chr7	124532319	124532434	115	-	jaccard	1.918e-12	0.36	0.35	35	96	22.84	6902.91	0	0.0	0.0	end	5.7541e-12	1.2885e-08	True		outrider,fraser						False	exonSkipping	inconclusive	3'-UTR	False

{scout-browser-4.87 → scout-browser-4.88}/scout/demo/drop/outrider_top_hits_clinical.tsv

@@ -1,10 +1,10 @@
-hgnc_id	seqnames	start	end	strand	geneID	hgncSymbol	gene_type	gene_name_orig	sampleID	pValue	padjust	zScore	l2fc	rawcounts	normcounts	meanCorrected	theta	aberrant	AberrantBySample	AberrantByGene	padj_rank	FDR_set	foldChange
-25415	chr4	88257620	88284769	-	ENSG00000163644.15	PPM1K	protein_coding	PPM1K	ADM1059A2	0.0016124374690447165	1.0	-5.92	-0.9	27	317.46	601.46	139.77	False	4.0	0.0	6110.0	transcriptome-wide	0.54
-10019	chr6	3063824	3115187	+	ENSG00000137275.16	RIPK1	protein_coding	RIPK1	ADM1059A2	0.0009997468998232232	1.0	6.33	0.53	104	1891.09	1308.4	547.35	False	4.0	0.0	6110.0	transcriptome-wide	1.44
-4827	chr11	5225464	5229395	-	ENSG00000244734.4	HBB	protein_coding	HBB	ADM1059A2	3.417496739472308e-25	4.169327890311004e-20	-12.61	-10.14	61	2625.42	3016434.64	9.21	True	4.0	1.0	1.0	transcriptome-wide	0.0
-4831	chr11	5248269	5249857	-	ENSG00000213934.9	HBG1	protein_coding	HBG1	ADM1059A3	0.0016205310428587193	1.0	2.23	2.86	73	151.01	19.19	0.91	False	4.0	0.0	6110.0	transcriptome-wide	7.26
-16860	chr12	108522214	108561400	-	ENSG00000075856.12	SART3	protein_coding	SART3	ADM1059A2	0.0014636643867152977	1.0	7.02	0.51	97	1412.71	989.2	1000.0	False	4.0	0.0	6110.0	transcriptome-wide	1.42
-4824	chr16	172876	173710	+	ENSG00000188536.13	HBA2	protein_coding	HBA2	ADM1059A2	2.15484140654196e-24	1.2729742965811128e-19	-12.53	-10.01	262	6781.29	7019330.9	8.97	True	4.0	1.0	2.5	transcriptome-wide	0.0
-4823	chr16	176680	177522	+	ENSG00000206172.8	HBA1	protein_coding	HBA1	ADM1059A2	3.1302782768232926e-24	1.2729742965811128e-19	-12.5	-9.97	246	6497.61	6540277.08	8.95	True	4.0	1.0	2.5	transcriptome-wide	0.0
-9543	chr17	4796144	4798502	+	ENSG00000142507.10	PSMB6	protein_coding	PSMB6	ADM1059A2	0.0010771639306525651	1.0	-10.54	-1.14	13	342.89	783.82	1000.0	False	4.0	0.0	6110.0	transcriptome-wide	0.45
-17284	chr7	124532319	124532434	-	ENSG00000213934.9	POT1	protein_coding	POT1	ADM1059A2	0.0016205310428587193	1.0	2.23	2.86	73	151.01	19.19	0.91	False	4.0	0.0	6110.0	transcriptome-wide	7.26
+hgncId	seqnames	start	end	strand	geneID	hgncSymbol	geneType	geneNameOrig	sampleID	pValue	padjust	zScore	l2fc	rawcounts	normcounts	meanCorrected	theta	aberrant	aberrantbysample	aberrantbygene	padjRank	FDRset	foldChange
+25415	chr4	88257620	88284769	-	ENSG00000163644.15	PPM1K	protein_coding	PPM1K	RNA1059A2	0.0016124374690447165	1.0	-5.92	-0.9	27	317.46	601.46	139.77	False	4.0	0.0	6110.0	transcriptome-wide	0.54
+10019	chr6	3063824	3115187	+	ENSG00000137275.16	RIPK1	protein_coding	RIPK1	RNA1059A2	0.0009997468998232232	1.0	6.33	0.53	104	1891.09	1308.4	547.35	False	4.0	0.0	6110.0	transcriptome-wide	1.44
+4827	chr11	5225464	5229395	-	ENSG00000244734.4	HBB	protein_coding	HBB	RNA1059A2	3.417496739472308e-25	4.169327890311004e-20	-12.61	-10.14	61	2625.42	3016434.64	9.21	True	4.0	1.0	1.0	transcriptome-wide	0.0
+4831	chr11	5248269	5249857	-	ENSG00000213934.9	HBG1	protein_coding	HBG1	RNA1059A3	0.0016205310428587193	1.0	2.23	2.86	73	151.01	19.19	0.91	False	4.0	0.0	6110.0	transcriptome-wide	7.26
+16860	chr12	108522214	108561400	-	ENSG00000075856.12	SART3	protein_coding	SART3	RNA1059A2	0.0014636643867152977	1.0	7.02	0.51	97	1412.71	989.2	1000.0	False	4.0	0.0	6110.0	transcriptome-wide	1.42
+4824	chr16	172876	173710	+	ENSG00000188536.13	HBA2	protein_coding	HBA2	RNA1059A2	2.15484140654196e-24	1.2729742965811128e-19	-12.53	-10.01	262	6781.29	7019330.9	8.97	True	4.0	1.0	2.5	transcriptome-wide	0.0
+4823	chr16	176680	177522	+	ENSG00000206172.8	HBA1	protein_coding	HBA1	RNA1059A2	3.1302782768232926e-24	1.2729742965811128e-19	-12.5	-9.97	246	6497.61	6540277.08	8.95	True	4.0	1.0	2.5	transcriptome-wide	0.0
+9543	chr17	4796144	4798502	+	ENSG00000142507.10	PSMB6	protein_coding	PSMB6	RNA1059A2	0.0010771639306525651	1.0	-10.54	-1.14	13	342.89	783.82	1000.0	False	4.0	0.0	6110.0	transcriptome-wide	0.45
+17284	chr7	124532319	124532434	-	ENSG00000213934.9	POT1	protein_coding	POT1	RNA1059A2	0.0016205310428587193	1.0	2.23	2.86	73	151.01	19.19	0.91	False	4.0	0.0	6110.0	transcriptome-wide	7.26

{scout-browser-4.87 → scout-browser-4.88}/scout/load/setup.py

@@ -158,8 +158,9 @@ def setup_scout(
         # Create a map from ensembl ids to gene objects
         ensembl_genes = {}
         for gene_obj in hgnc_genes:
-            ensembl_id = gene_obj["ensembl_id"]
-            ensembl_genes[ensembl_id] = gene_obj
+            ensembl_id = gene_obj.get("ensembl_id")
+            if ensembl_id:
+                ensembl_genes[ensembl_id] = gene_obj
 
         # Load transcripts
         tx_path = "transcripts{}_path".format(build)

{scout-browser-4.87 → scout-browser-4.88}/scout/models/case/case.py

@@ -31,6 +31,7 @@ individual = dict(
     smn_27134_cn=int,  # CopyNumber
     rna_alignment_path=str,  # Path to bam file
     rna_coverage_bigwig=str,  # Coverage islands generated from bam or cram files (RNA-seq analysis)
+    omics_sample_id=str,  # RNA sample id for connected wts outliers
     splice_junctions_bed=str,  # An indexed junctions .bed.gz file obtained from STAR v2 aligner *.SJ.out.tab file.
     predicted_ancestry=str,  # one of AFR AMR EAS EUR SAS UNKNOWN
     tumor_type=str,

{scout-browser-4.87 → scout-browser-4.88}/scout/models/case/case_loading_models.py

@@ -221,6 +221,7 @@ class SampleLoader(BaseModel):
     rhocall_wig: Optional[str] = None
     rna_alignment_path: Optional[str] = None
     rna_coverage_bigwig: Optional[str] = None
+    omics_sample_id: Optional[str] = None
     sample_name: Optional[str] = None
     sex: Literal["unknown", "female", "male"]
     smn1_cn: Optional[int] = None

{scout-browser-4.87 → scout-browser-4.88}/scout/models/omics_variant.py

@@ -9,7 +9,7 @@ import logging
 from datetime import datetime
 from typing import List, Optional
 
-from pydantic import BaseModel, Field, field_validator, model_validator
+from pydantic import AliasChoices, BaseModel, Field, field_validator, model_validator
 
 LOG = logging.getLogger(__name__)
 
@@ -38,18 +38,28 @@ class OmicsVariantLoader(BaseModel):
 
     # sample id is mandatory: each row pertains to one outlier event in one individual as compared to others
     # In the db object, this will be replaced with a "samples" array of individual dict.
-    sampleID: str
+    sample_id: str = Field(
+        alias=AliasChoices("sample_id", "sampleID"), serialization_alias="sample_id"
+    )
 
     # outlier variants must identify the gene they pertain to, primarily with an hgnc_id
-    hgnc_ids: Optional[List[int]] = Field(alias="hgnc_id", serialization_alias="hgnc_ids")
-    geneID: Optional[str]
+    hgnc_ids: Optional[List[int]] = Field(alias="hgncId", serialization_alias="hgnc_ids")
+    ensembl_gene_id: Optional[str] = Field(
+        alias="geneID", serialization_alias="ensembl_gene_id", default=None
+    )
 
     hgnc_symbols: Optional[List[str]] = Field(
         alias="hgncSymbol", serialization_alias="hgnc_symbols"
     )
-    gene_name_orig: Optional[str]
+    gene_name_orig: Optional[str] = Field(
+        alias=AliasChoices("geneNameOrig", "gene_name_orig"),
+        serialization_alias="gene_name_orig",
+        default=None,
+    )
 
-    gene_type: Optional[str]
+    gene_type: Optional[str] = Field(
+        alias=AliasChoices("gene_type", "geneType"), serialization_alias="gene_type", default=None
+    )
 
     # coordinates if applicable
     chromosome: Optional[str] = Field(alias="seqnames", serialization_alias="chromosome")
@@ -85,7 +95,7 @@ class OmicsVariantLoader(BaseModel):
         alias="nonsplitProportion", serialization_alias="nonsplit_proportion", default=None
     )
     nonsplit_proportion_99quantile: Optional[float] = Field(
-        alias="nonsplitProportion_99quantile",
+        alias="nonsplitproportion99quantile",
         serialization_alias="nonsplit_proportion_99quantile",
         default=None,
     )
@@ -99,7 +109,7 @@ class OmicsVariantLoader(BaseModel):
         alias="padjustGene", serialization_alias="p_adjust_gene", default=None
     )
     paired_end: Optional[str] = Field(
-        alias="PAIRED_END", serialization_alias="paired_end", default=None
+        alias="pairedEnd", serialization_alias="paired_end", default=None
     )
     is_external: Optional[bool] = Field(
         alias="isExternal", serialization_alias="is_external", default=None
@@ -111,16 +121,22 @@ class OmicsVariantLoader(BaseModel):
         alias="causesFrameshift", serialization_alias="causes_frameshift", default=None
     )
     utr_overlap: Optional[str] = Field(
-        alias="UTR_overlap", serialization_alias="utr_overlap", default=None
+        alias="utrOverlap", serialization_alias="utr_overlap", default=None
     )
 
     # Outrider specific
     padjust: Optional[float] = None
     zscore: Optional[float] = Field(alias="zScore", serialization_alias="zscore", default=None)
     l2fc: Optional[float] = None
-    rawcounts: Optional[int] = None
-    normcounts: Optional[float] = None
-    meanCorrected: Optional[float] = None
+    raw_counts: Optional[int] = Field(
+        alias="rawcounts", serialization_alias="raw_counts", default=None
+    )
+    norm_counts: Optional[float] = Field(
+        alias="normcounts", serialization_alias="norm_counts", default=None
+    )
+    mean_corrected: Optional[float] = Field(
+        alias="meanCorrected", serialization_alias="mean_corrected", default=None
+    )
     theta: Optional[float] = None
     aberrant: Optional[bool] = None
     aberrant_by_sample: Optional[float] = Field(
@@ -135,6 +151,13 @@ class OmicsVariantLoader(BaseModel):
         alias="foldChange", serialization_alias="fold_change", default=None
     )
 
+    @model_validator(mode="before")
+    @classmethod
+    def empty_str_to_none(cls, values):
+        if isinstance(values, dict):
+            return {k: (None if v == "" else v) for k, v in values.items()}
+        return values
+
     @field_validator("chromosome")
     def strip_chr(cls, chrom: str) -> str:
         """We store chromosome names without a chr prefix internally."""
@@ -162,8 +185,10 @@ class OmicsVariantLoader(BaseModel):
         """HGNC ids and gene symbols are found one on each line in DROP tsvs.
         Convert to a list with a single member in omics_variants for storage."""
 
-        if "hgnc_id" in values:
-            values["hgnc_id"] = [int(values.get("hgnc_id"))]
+        if "hgncId" in values:
+            values["hgncId"] = [int(values.get("hgncId"))]
+        elif "hgnc_id" in values:
+            values["hgncId"] = [int(values.get("hgnc_id"))]
 
         if "hgncSymbol" in values:
             values["hgncSymbol"] = [str(values.get("hgncSymbol"))]
@@ -206,14 +231,6 @@ class OmicsVariantLoader(BaseModel):
         )
         return values
 
-    @model_validator(mode="before")
-    def set_sample_display_name(cls, values) -> "OmicsVariantLoader":
-        """Set a display name."""
-        values["display_name"] = values.get(
-            "display_name", values.get("sample_name", values.get("individual_id"))
-        )
-        return values
-
 
 def get_qualification(values: dict) -> str:
     """Get qualification string for ID and display name.

{scout-browser-4.87 → scout-browser-4.88}/scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html

@@ -109,7 +109,12 @@
                 {% endif %}
               </td>
               <td class="text-end">{{ '%.3e' % variant.p_value }}</td>
-              <td>{{ case.individuals.0.display_name }}</td>
+              <td>{% for sample in variant.samples %}
+                  {% if sample.genotype_call != "./." %}
+                    <div>{{ sample.display_name }}</div>
+                  {% endif %}
+                {% endfor %}
+              </td>
               <td class="text-end">{{ variant.chromosome }}</td>
                 <td class="text-end"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span>-<span style="white-space: nowrap;">{{ variant.end|human_longint|safe }}</span>
                 {% if case.has_rna_tracks %}

{scout-browser-4.87 → scout-browser-4.88}/scout/server/blueprints/variant/templates/variant/sv-variant.html

@@ -2,7 +2,7 @@
 {% from "utils.html" import activity_panel, comments_panel, pedigree_panel %}
 {% from "variant/variant_details.html" import old_observations %}
 {% from "variant/components.html" import external_scripts, external_stylesheets, matching_variants, variant_scripts %}
-{% from "variant/utils.html" import causative_button, genes_panel, igv_track_selection, modal_causative, overlapping_panel, sv_alignments, pin_button, transcripts_panel, custom_annotations %}
+{% from "variant/utils.html" import causative_button, genes_panel, igv_track_selection, modal_causative, overlapping_panel, sv_alignments, pin_button, transcripts_panel, custom_annotations, gene_panels %}
 {% from "variant/rank_score_results.html" import rankscore_panel %}
 {% from "variant/gene_disease_relations.html" import orpha_omim_phenotypes %}
 {% from "variant/variant_details.html" import frequencies, gtcall_panel, observations_panel %}
@@ -189,10 +189,7 @@
         {% endif %}
 
         <div class="list-group-item">
-          <strong>Gene panels:</strong><br>
-          {% for panel_id in variant.panels|sort(case_sensitive=False) %}
-            <a href="{{ url_for('panels.panel', panel_id=panel_id) }}">{{ panel_id }}</a>&nbsp;&nbsp;
-          {% endfor %}
+          {{ gene_panels(variant) }}
         </div>
         <div class="list-group mt-3">
           <div>

{scout-browser-4.87 → scout-browser-4.88}/scout/server/blueprints/variant/templates/variant/utils.html

@@ -443,3 +443,52 @@
 	</tbody>
 </table>
 {% endmacro %}
+
+
+{% macro gene_panels(variant) %}
+<strong>Gene panels:</strong><br>
+{% for panel in variant.case_panels|sort(attribute='panel_name', case_sensitive=False)|rejectattr('removed') %}
+  {% set symbol_genes_counter = namespace(value=0) %}
+  {% set nosymbol_genes_counter = namespace(value=0) %}
+  <a
+    href="{{ url_for('panels.panel', panel_id=panel.panel_id) }}"
+    {#
+    Add hovertip listing occurence of each gene on selected panels, in the case
+    where variant covers multiple genes.
+    #}
+    {% if (variant.genes | length) > 1 %}
+      class="badge bg-secondary text-white"
+      data-bs-original-title="Genes on gene panel"
+      data-bs-toggle="popover"
+      data-bs-html="true"
+      data-bs-trigger="hover click"
+      data-bs-content="
+
+        {% for gene in variant.genes %}
+          {% if panel['panel_name'] in gene['associated_gene_panels'] %}
+            {% if symbol_genes_counter.value <= 30 %}
+              {% if gene.common %}
+                {{ gene.common.hgnc_symbol }}
+              {% else %}
+                {% for panel_gene in panel.genes %}
+                  {% if gene.hgnc_id == panel_gene.hgnc_id %}
+                    {{ panel_gene.symbol + "&nbsp;" }}
+                  {% endif %}
+                {% endfor %}
+              {% endif %}
+              {% set symbol_genes_counter.value = symbol_genes_counter.value +1 %}
+            {% else %}
+              {% set nosymbol_genes_counter.value = nosymbol_genes_counter.value +1 %}
+            {% endif %}
+          {% endif %}
+        {% endfor %}
+
+        {% if nosymbol_genes_counter.value %}
+         + {{nosymbol_genes_counter.value}} other genes
+        {% endif %}
+
+      "
+    {% endif %}
+  >{{ panel.panel_name }}</a>&nbsp;&nbsp;
+{% endfor %}
+{% endmacro %}

{scout-browser-4.87 → scout-browser-4.88}/scout/server/blueprints/variant/templates/variant/variant.html

@@ -2,7 +2,7 @@
 {% from "variant/buttons.html" import database_buttons %}
 {% from "utils.html" import activity_panel, comments_panel, pedigree_panel %}
 {% from "variants/utils.html" import compounds_table %}
-{% from "variant/utils.html" import causative_button, genes_panel, modal_causative, overlapping_panel, pin_button, proteins_panel, transcripts_panel, custom_annotations %}
+{% from "variant/utils.html" import causative_button, genes_panel, modal_causative, overlapping_panel, pin_button, proteins_panel, transcripts_panel, custom_annotations, gene_panels %}
 {% from "variant/tx_overview.html" import disease_associated, transcripts_overview %}
 {% from "variant/gene_disease_relations.html" import autozygosity_panel, genemodels_panel, inheritance_panel, orpha_omim_phenotypes %}
 {% from "variant/variant_details.html" import conservations, frequencies, gtcall_panel, mappability, observations_panel, old_observations, severity_list, str_db_card %}
@@ -373,30 +373,7 @@
       </table>
       <ul class="list-group">
         <div class="list-group-item">
-          <strong>Gene panels:</strong><br>
-          {% for panel in variant.case_panels|sort(attribute='panel_name', case_sensitive=False)|rejectattr('removed') %}
-            <a
-              href="{{ url_for('panels.panel', panel_id=panel.panel_id) }}"
-              {#
-              Add hovertip listing occurence of each gene on selected panels, in the case
-              where variant covers multiple genes.
-              #}
-              {% if (variant.genes | length) > 1 %}
-              class="badge bg-secondary text-white"
-              data-bs-original-title="Genes on gene panel"
-              data-bs-toggle="popover"
-              data-bs-html="true"
-              data-bs-trigger="hover click"
-              data-bs-content="
-              {% for gene in variant.genes %}
-                {% if panel['panel_name'] in gene['associated_gene_panels'] %}
-                  {{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
-                {% endif%}
-              {%endfor%}
-              "
-              {% endif %}
-            >{{ panel.panel_name }}</a>&nbsp;&nbsp;
-          {% endfor %}
+          {{ gene_panels(variant) }}
         </div>
       </ul>
       {% if variant.category != "str" %}

{scout-browser-4.87 → scout-browser-4.88}/scout/server/blueprints/variant/utils.py

@@ -612,12 +612,19 @@ def callers(variant_obj):
 def associate_variant_genes_with_case_panels(case_obj: Dict, variant_obj: Dict) -> None:
     """Add associated gene panels to each gene in variant object"""
 
-    genes = variant_obj.get("genes", [])
+    geneid_gene: Dict[int, dict] = {
+        gene["hgnc_id"]: gene for gene in variant_obj.get("genes", [])
+    }  # This has max 30 elements for SVs
+    geneids: List[int] = variant_obj.get("hgnc_ids", [])  # This can be a long list, n > 30 for SVs
 
-    for gene in genes:
-        hgnc_id = gene["hgnc_id"]
+    for hgnc_id in geneids:
         matching_panels = []
         for panel in case_obj.get("latest_panels", []):
             if hgnc_id in panel["hgnc_ids"]:
                 matching_panels.append(panel["panel_name"])
-        gene["associated_gene_panels"] = matching_panels
+        if hgnc_id not in geneid_gene:
+            geneid_gene[hgnc_id] = {"hgnc_id": hgnc_id, "associated_gene_panels": matching_panels}
+        else:
+            geneid_gene[hgnc_id]["associated_gene_panels"] = matching_panels
+
+    variant_obj["genes"] = list(geneid_gene.values())

{scout-browser-4.87 → scout-browser-4.88}/scout/server/blueprints/variants/templates/variants/components.html

@@ -143,7 +143,7 @@
 {% endmacro %}
 
 {% macro gene_cell(variant) %}
-  <div class="d-flex align-items-center">
+  <div class="align-items-center">
     {% if variant.category == "cancer" or variant.category == "sv_cancer" %}
       <a data-bs-toggle="tooltip" data-bs-html="true" title="
         <div>
@@ -367,6 +367,10 @@
         {{ variant.max_exac_frequency|human_decimal if variant.max_exac_frequency }}
       </div>
       {% endif %}
+      {% if 'colorsdb_af' in variant %}
+        <strong>CoLoRSdb</strong>:
+        {{ variant.colorsdb_af|human_decimal if variant.colorsdb_af }}
+      {% endif %}
     </div>
   ">
   <div>

{scout-browser-4.87 → scout-browser-4.88/scout_browser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.87
+Version: 4.88
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.87/scout/__version__.py

@@ -1 +0,0 @@
-__version__ = "4.87"

scout-browser-4.87/scout/demo/drop/fraser_top_hits_clinical.tsv

@@ -1,5 +0,0 @@
-hgnc_id	geneID	hgncSymbol	gene_type	gene_name_orig	sampleID	seqnames	start	end	width	strand	type	pValue	psiValue	deltaPsi	counts	totalCounts	meanCounts	meanTotalCounts	nonsplitCounts	nonsplitProportion	nonsplitProportion_99quantile	annotatedJunction	pValueGene	padjustGene	PAIRED_END	DNA_ID	DROP_GROUP	SPLICE_COUNTS_DIR	HPO_TERMS	GENE_COUNTS_FILE	GENE_ANNOTATION	GENOME	isExternal	potentialImpact	causesFrameshift	UTR_overlap	blacklist
-2439	ENSG00000119535.18	CSF3R	protein_coding	CSF3R	ADM1059A2	chr1	36479517	Imp	1961	-	jaccard	1.6652e-06	0.49	-0.39	127	258	4237.77	4570.55	3	0.01	0.02	both	9.9912e-06	0.013423	True		outrider,fraser						False	annotatedIntron_reducedUsage	unlikely	5'-UTR	False
-4831	ENSG00000213934.9	HBG1	protein_coding	HBG1	ADM1059A2	chr11	5248488	5254291	5804	-	jaccard	1.918e-12	0.36	0.35	35	96	22.84	6902.91	0	0.0	0.0	end	5.7541e-12	1.2885e-08	True		outrider,fraser						False	exonSkipping	inconclusive	3'-UTR	False
-4832	ENSG00000196565.15	HBG2	protein_coding	HBG2	ADM1059A2	chr11	5248488	5254291	5804	-	jaccard	1.918e-12	0.36	0.35	35	96	22.84	6902.91	0	0.0	0.0	end	3.836e-12	1.2885e-08	True		outrider,fraser						False	exonSkipping	inconclusive	3'-UTR	False
-17284	ENSG00000213934.9	POT1	protein_coding	POT1	ADM1059A2	chr7	124532319	124532434	115	-	jaccard	1.918e-12	0.36	0.35	35	96	22.84	6902.91	0	0.0	0.0	end	5.7541e-12	1.2885e-08	True		outrider,fraser						False	exonSkipping	inconclusive	3'-UTR	False