scout-browser 4.81__py3-none-any.whl → 4.82.1__py3-none-any.whl

scout/server/blueprints/variant/templates/variant/variant.html

@@ -5,7 +5,7 @@
 {% from "variant/utils.html" import causative_button, genes_panel, modal_causative, overlapping_panel, pin_button, proteins_panel, transcripts_panel, custom_annotations %}
 {% 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 frequencies, gtcall_panel, old_observations, observations_panel, severity_list, conservations, mappability %}
+{% from "variant/variant_details.html" import conservations, frequencies, gtcall_panel, mappability, observations_panel, old_observations, severity_list, str_db_card %}
 {% from "variant/components.html" import alignments, clinsig_table, compounds_panel, external_links, external_scripts, external_stylesheets, matching_variants, panel_classify, variant_scripts %}
 {% from "variant/sanger.html" import modal_cancel_sanger, modal_sanger, sanger_button %}
 {% from "variant/rank_score_results.html" import rankscore_panel %}
@@ -90,11 +90,15 @@
         {{ panel_summary() }}
       </div>
       <div class="col-lg-4">
-        {{ frequencies(variant) }}
-        {% if config['LOQUSDB_SETTINGS'] %}
-          {{ observations_panel(variant, observations, case) }}
+        {% if str %}
+          {{ str_db_card(variant) }}
+        {% else %}
+          {{ frequencies(variant) }}
+          {% if config['LOQUSDB_SETTINGS'] %}
+            {{ observations_panel(variant, observations, case) }}
+          {% endif %}
+          {{  old_observations(variant) }}
         {% endif %}
-        {{  old_observations(variant) }}
       </div>
     </div>
     <div class="row">
@@ -227,8 +231,8 @@
           <tr>
             <td>
               Position:
-	      <strong>{{ variant.chromosome }}:<span class="text-muted">{{ variant.position }}</span></strong>
-             <button type="button" class="fa fa-copy btn-xs js-tooltip js-copy" style="background-color: Transparent;outline:none; border: none;" data-bs-toggle="tooltip" data-bs-placement="bottom" data-copy="{{ variant.chromosome }}:{{ variant.position }}" title="Copy to clipboard">
+	            <strong>{{ variant.chromosome }}:<span class="text-muted">{{ variant.position }}</span></strong>
+              <button type="button" class="fa fa-copy btn-xs js-tooltip js-copy" style="background-color: Transparent;outline:none; border: none;" data-bs-toggle="tooltip" data-bs-placement="bottom" data-copy="{{ variant.chromosome }}:{{ variant.position }}" title="Copy to clipboard">
               </button>
             </td>
             <td {% if not mei %}colspan="3"{% endif %}>
@@ -282,13 +286,12 @@
               </strong></span>
             </td>
           </tr>
-
         </tbody>
       </table>
       <table class="table table-bordered table-fixed table-sm">
         <tbody class="border-top">
           <tr>
-            <td>
+            <td {% if str %}colspan="2"{% endif %}>
               Matches OMIM inhert.
               {% if variant.is_matching_inheritance %}
                 <span class="badge bg-success float-end">Yes</span>
@@ -296,12 +299,14 @@
                 <div class="badge bg-warning float-end">No</div>
               {% endif %}
             </td>
-            <td>
-              Frequency
-              <div class="badge bg-{% if variant.frequency == 'common' %}danger{% elif variant.frequency == 'uncommon' %}warning{% else %}success{% endif %} float-end">
-                {{ variant.frequency }}
-              </div>
-            </td>
+            {% if not str %}
+              <td>
+                Frequency
+                <div class="badge bg-{% if variant.frequency == 'common' %}danger{% elif variant.frequency == 'uncommon' %}warning{% else %}success{% endif %} float-end">
+                  {{ variant.frequency }}
+                </div>
+              </td>
+            {% endif %}
           </tr>
         </tbody>
       </table>

scout/server/blueprints/variant/templates/variant/variant_details.html

@@ -105,37 +105,89 @@
   </div>
 {% endmacro %}
 
-{% macro frequencies(variant) %}
+{% macro str_db_card(variant) %}
   <div class="card panel-default">
-    <div class="panel-heading">Frequencies</div>
+    <div class="panel-heading">STR locus details</div>
     <div class="card-body">
-      <table class="table">
+      <table class="table" aria-label="STR locus details">
         <thead class="thead table-light">
-          <tr>
-            <th scope="col">Source</th>
-            <th scope="col">Frequency</th>
-          </tr>
-        </thead>
-        <tbody>
-          {% for freq_name, value, link in variant.frequencies %}
-          <tr>
-            <td>
-              {% if link %}
-                <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
-              {% else %}
-                {{ freq_name }}
+            <tr>
+              <th scope="col">Source</th>
+              <th scope="col">Value</th>
+            </tr>
+          </thead>
+          <tbody>
+            <tr><td>Normal max</td><td>{{ variant.str_normal_max }}</td></tr>
+            <tr><td>Pathologic min</td><td>{{ variant.str_pathologic_min }}</td><tr>
+            {% if variant.str_status == 'full_mutation' %}
+              <tr class="bg-danger">
+            {% elif variant.str_status == 'pre_mutation' %}
+              <tr class="bg-warning">
+            {% else %}
+              <tr>
+	          {% endif %}
+              <td>Motif copies</td><td>{{ variant.str_mc }} <span class="badge bg-secondary text-white">{{ variant.str_status }}</span></td>
+            </tr>
+            <tr><td colspan=2>&nbsp;</td></tr>
+            {% if variant.str_swegen_mean %}
+              <tr><td>SweGen Z-score</td><td>
+                {% if variant.str_mc %}
+                  {{ ((variant.str_mc - variant.str_swegen_mean ) / variant.str_swegen_std) | round(2) }}
+                {% endif %}
+              </td></tr>
+              <tr><td>SweGen mean</td><td>{{variant.str_swegen_mean|round(2)}}</td></tr>
+              <tr><td>SweGen std</td><td>{{variant.str_swegen_std|round(2)}}</td></tr>
+              <tr><td colspan=2>&nbsp;</td></tr>
+            {% endif %}
+            {% for gene in variant.genes %}
+              {% if gene.stripy_link %}
+                <tr><td>
+                  <a href="{{ gene.str_gnomad_link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">gnomAD</a>
+                </td><td>{{ gene.hgnc_symbol }}</td></tr>
               {% endif %}
-            </td>
-            <td>
-              {% if value %}
-                <span class="badge bg-secondary">{{ value|human_decimal }}</span>
-              {% else %}
-                -
+              {% if gene.stripy_link %}
+                <tr><td>
+                  <a href="{{ gene.stripy_link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">STRipy</a>
+                </td><td>{{ gene.hgnc_symbol }}</td></tr>
               {% endif %}
-            </td>
-          </tr>
-          {% endfor %}
-        </tbody>
+            {% endfor %}
+          </tbody>
+        </table>
+    </div>
+  </div>
+{% endmacro %}
+
+{% macro frequencies(variant) %}
+  <div class="card panel-default">
+    <div class="panel-heading">Frequencies</div>
+    <div class="card-body">
+      <table class="table">
+          <thead class="thead table-light">
+            <tr>
+              <th scope="col">Source</th>
+              <th scope="col">Frequency</th>
+            </tr>
+          </thead>
+          <tbody>
+            {% for freq_name, value, link in variant.frequencies %}
+              <tr>
+                <td>
+                  {% if link %}
+                    <a href="{{ link }}" target="_blank" rel="noopener" referrerpolicy="no-referrer">{{ freq_name }}</a>
+                  {% else %}
+                    {{ freq_name }}
+                  {% endif %}
+                </td>
+                <td>
+                  {% if value %}
+                    <span class="badge bg-secondary">{{ value|human_decimal }}</span>
+                  {% else %}
+                    -
+                  {% endif %}
+                </td>
+              </tr>
+            {% endfor %}
+          </tbody>
       </table>
     </div>
   </div>

scout/server/blueprints/variant/utils.py

@@ -175,15 +175,13 @@ def update_variant_case_panels(case_obj: dict, variant_obj: dict):
     The case_obj should be up-to-date first. Call update_case_panels() as needed in context:
     to save some resources we do not call it here for each variant.
     """
-
+    variant_obj["case_panels"] = []
     variant_panel_names = variant_obj.get("panels") or []
-    case_panel_objs = [
-        panel
-        for panel in (case_obj.get("panels") or [])
-        if panel["panel_name"] in variant_panel_names
-    ]
-
-    variant_obj["case_panels"] = case_panel_objs
+    for latest_panel in case_obj.get("latest_panels") or []:
+        if latest_panel["panel_name"] not in variant_panel_names:
+            continue
+        if not set(latest_panel["hgnc_ids"]).isdisjoint(variant_obj["hgnc_ids"]):
+            variant_obj["case_panels"].append(latest_panel)
 
 
 def get_extra_info(gene_panels: list) -> Dict[int, dict]:
@@ -660,17 +658,15 @@ def callers(variant_obj):
     return list(calls)
 
 
-def associate_variant_genes_with_case_panels(store: MongoAdapter, variant_obj: Dict) -> None:
+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", [])
-    gene_panels = variant_obj.get("case_panels", [])
 
     for gene in genes:
         hgnc_id = gene["hgnc_id"]
         matching_panels = []
-        for panel in gene_panels:
-            genes_on_panel = store.panel_to_genes(panel_id=panel["panel_id"], gene_format="hgnc_id")
-            if hgnc_id in genes_on_panel:
+        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

scout/server/blueprints/variants/controllers.py

@@ -51,6 +51,8 @@ from scout.server.utils import (
 from .forms import FILTERSFORMCLASS, CancerSvFiltersForm, FusionFiltersForm, SvFiltersForm
 from .utils import update_case_panels
 
+NUM = re.compile(r"\d+")
+
 LOG = logging.getLogger(__name__)
 
 
@@ -938,6 +940,10 @@ def parse_variant(
     if not "end_chrom" in variant_obj:
         variant_obj["end_chrom"] = variant_obj["chromosome"]
 
+    # common motif count for STR variants
+
+    variant_obj["str_mc"] = get_str_mc(variant_obj)
+
     # variant level links shown on variants page
     variant_obj["cosmic_links"] = cosmic_links(variant_obj)
     variant_obj["str_source_link"] = str_source_link(variant_obj)
@@ -959,6 +965,31 @@ def parse_variant(
     return variant_obj
 
 
+def get_str_mc(variant_obj: dict) -> Optional[int]:
+    """Return variant Short Tandem Repeat motif count, either as given by its ALT MC value
+    from the variant FORMAT field, or as a number given in the ALT on the form
+    '<STR123>'.
+    """
+
+    alt_mc = None
+    if variant_obj["alternative"] == ".":
+        return alt_mc
+
+    for sample in variant_obj["samples"]:
+        if sample["genotype_call"] in ["./.", ".|", "0/0", "0|0"]:
+            continue
+        alt_mc = sample.get("alt_mc")
+    if alt_mc:
+        return alt_mc
+
+    alt_num = NUM.match(variant_obj["alternative"])
+    if alt_num:
+        alt_mc = int(alt_num)
+        return alt_mc
+
+    return None
+
+
 def download_str_variants(case_obj, variant_objs):
     """Download filtered STR variants for a case to a CSV file
 
@@ -995,9 +1026,7 @@ def download_str_variants(case_obj, variant_objs):
         variant_line.append(
             variant.get("str_display_ru", variant.get("str_ru", ""))
         )  # Reference repeat unit
-        variant_line.append(
-            variant.get("alternative", "").replace("STR", "").replace("<", "").replace(">", "")
-        )  # Estimated size
+        variant_line.append(get_str_mc(variant) or ".")  # Estimated size
         variant_line.append(str(variant.get("str_ref", "")))  # Reference size
         variant_line.append(str(variant.get("str_status", "")))  # Status
         gt_cell = ""

scout/server/blueprints/variants/forms.py

@@ -95,6 +95,7 @@ class VariantFiltersForm(FlaskForm):
     variant_type = HiddenField(default="clinical")
 
     gene_panels = NonValidatingSelectMultipleField(choices=[])
+    gene_panels_exclude = BooleanField("Exclude genes")
     hgnc_symbols = TagListField("HGNC Symbols/Ids (case sensitive)")
 
     region_annotations = SelectMultipleField(choices=REGION_ANNOTATIONS)
@@ -111,7 +112,7 @@ class VariantFiltersForm(FlaskForm):
     clinsig = NonValidatingSelectMultipleField("ClinVar CLINSIG", choices=CLINSIG_OPTIONS)
 
     gnomad_frequency = BetterDecimalField("gnomadAF", validators=[validators.Optional()])
-    local_obs = IntegerField("Local obs. (archive)", validators=[validators.Optional()])
+    local_obs_old = IntegerField("Local obs. (archive)", validators=[validators.Optional()])
 
     filters = NonValidatingSelectField(choices=[], validators=[validators.Optional()])
     filter_display_name = StringField(default="")
@@ -165,6 +166,12 @@ class CancerFiltersForm(VariantFiltersForm):
     clinvar_tag = BooleanField("ClinVar hits")
     cosmic_tag = BooleanField("Cosmic hits")
     mvl_tag = BooleanField("Managed Variants hits")
+    local_obs_cancer_somatic_old = IntegerField(
+        "Local somatic obs. (archive)", validators=[validators.Optional()]
+    )
+    local_obs_cancer_germline_old = IntegerField(
+        "Local germline obs. (archive)", validators=[validators.Optional()]
+    )
 
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE_CANCER
@@ -196,6 +203,13 @@ class SvFiltersForm(VariantFiltersForm):
     swegen = IntegerField("SweGen obs")
     clinical_filter = SubmitField(label="Clinical filter")
 
+    local_obs_cancer_somatic_old = IntegerField(
+        "Local somatic obs. (archive)", validators=[validators.Optional()]
+    )
+    local_obs_cancer_germline_old = IntegerField(
+        "Local germline obs. (archive)", validators=[validators.Optional()]
+    )
+
     # polymorphic constant base for clinical filter
     clinical_filter_base = CLINICAL_FILTER_BASE_SV
 

scout/server/blueprints/variants/templates/variants/components.html

@@ -23,6 +23,61 @@
   </div>
 {% endmacro %}
 
+{% macro fusion_variants_header() %}
+  <thead class="table-light">
+    <tr>
+      <th id="checkbox" style="width:1%"></th>
+      <th id="rank" style="width:3%;" title="Beta version. Currently testing" class="text-left">Rank (beta)</th>
+      <th id="genes" style="width:6%" title="Genes">Fusion Genes</th>
+      <th id="callers" style="width:4%" title="Number of callers detecting a given event">Callers</th>
+      <th id="observed" style="width:4%" title="Observed database matches">Observed</th>
+      <th id="score" style="width:4%" title="Beta version. Currently testing">Score (beta)</th>
+      <th id="junction_reads" style="width:6%" title="Number of paired-ends that support the event">Junction Reads</th>
+      <th id="split_reads" style="width:6%" title="Number of split reads that support the event">Split Reads</th>
+      <th id="ffpm" style="width:6%" title="Fusion fragments per million total RNA-seq fragments">FFPM</th>
+      <th id="frame_status" style="width:8%" title="Frame status of the fusion">Frame Status</th>
+      <th id="transcripts" style="width:8%" title="Transcript ID">Transcript ID</th>
+      <th id="exons" style="width:4%" title="Exon Number">Exon Number</th>
+      <th id="brealpoints" style="width:4%" title="Breakpoints">Breakpoints</th>
+      <th id="oriantation" style="width:4%" title="Orientation">Orientation</th>
+    </tr>
+  </thead>
+{% endmacro %}
+
+{% macro default_fusion_variant_cells(institute, case, variant) %}
+  <td>
+    {{ fusion_variant_gene_symbols_cell(variant) }}
+  </td>
+  <td class="text-center"><span data-bs-toggle="tooltip" data-bs-html="true" title="{% for name, caller in variant.callers %}{{ name }}: {{ caller }}<br>{% endfor %}">
+    {{ variant.tool_hits|int }}</span></td>
+  <td>{{variant.found_db|join(", ") if variant.found_db else "-"}}</td>
+  <td class="text-center">{{ variant.fusion_score|float|round(3) }}</td>
+  <td class="text-center">{{ variant.samples[0].read_depth }}</td>
+  <td class="text-center">{{ variant.samples[0].split_read }}</td>
+  <td class="text-center">{{ variant.samples[0].ffpm }}</td>
+  <td>{{ variant.frame_status }}</td>
+  <td>
+    {% if variant.genes %}
+      {% for gene in variant.genes %}
+        {% for transcript in gene.transcripts %}
+          <div>{{ transcript.transcript_id }} </div>
+        {% endfor %}
+      {% endfor %}
+    {% endif %}
+  </td>
+  <td>
+    {% if variant.genes %}
+      {% for gene in variant.genes %}
+        {% for transcript in gene.transcripts %}
+          <div>{% if "exon" in transcript %}{{ transcript.exon|int }}{% endif %} </div>
+        {% endfor %}
+      {% endfor %}
+    {% endif %}
+  </td>
+  <td> {{ variant.chromosome }}:{{ variant.position }}  <br> {{ variant.end_chrom }}:{{ variant.end }} </td>
+  <td class="text-center">{{ variant.orientation }}</td>
+{% endmacro %}
+
 {% macro fusion_variant_gene_symbols_cell(variant) %}
 <div class="align-items-center">
   {% if variant.genes %}

scout/server/blueprints/variants/templates/variants/fusion-variants.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import fusion_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, fusion_variant_gene_symbols_cell %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, fusion_variant_gene_symbols_cell, fusion_variants_header, default_fusion_variant_cells %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - Fusion variants
@@ -54,24 +54,7 @@ onsubmit="return validateForm()">
 
     <div class="card mt-3">
       <table id="variantsTable" class="table table-hover table-bordered" aria-label="Fusion variants table">
-        <thead class="table-light thead">
-          <tr>
-            <th style="width:3%"></th>
-            <th style="width:4%" title="Beta version. Currently testing">Rank (beta)</th>
-            <th style="width:6%" title="Genes">Fusion Genes</th>
-            <th style="width:4%" title="Number of callers detecting a given event">Callers</th>
-            <th style="width:4%" title="Observed database matches">Observed</th>
-            <th style="width:4%" title="Beta version. Currently testing">Score (beta)</th>
-            <th style="width:6%" title="Number of paired-ends that support the event">Junction Reads</th>
-            <th style="width:6%" title="Number of split reads that support the event">Split Reads</th>
-            <th style="width:6%" title="Fusion fragments per million total RNA-seq fragments">FFPM</th>
-            <th style="width:8%" title="Frame status of the fusion">Frame Status</th>
-            <th style="width:8%" title="Transcript ID">Transcript ID</th>
-            <th style="width:4%" title="Exon Number">Exon Number</th>
-            <th style="width:4%" title="Breakpoints">Breakpoints</th>
-            <th style="width:4%" title="Orientation">Orientation</th>
-          </tr>
-        </thead>
+        {{ fusion_variants_header() }}
         <tbody>
           {% for variant in variants %}
             {{ variant_row(variant) }}
@@ -103,37 +86,7 @@ onsubmit="return validateForm()">
     <td class="text-start">
       {{ cell_rank(variant, institute, case, form, manual_rank_options) }}
     </td>
-    <td>
-      {{ fusion_variant_gene_symbols_cell(variant) }}
-    </td>
-    <td><span data-bs-toggle="tooltip" data-bs-html="true" title="{% for name, caller in variant.callers %}{{ name }}: {{ caller }}<br>{% endfor %}">
-      {{ variant.tool_hits|int }}</span></td>
-    <td>{{variant.found_db|join(", ") if variant.found_db else "-"}}</td>
-    <td class="text-end">{{ variant.fusion_score|float|round(3) }}</td>
-    <td>{{ variant.samples[0].read_depth }}</td>
-    <td>{{ variant.samples[0].split_read }}</td>
-    <td>{{ variant.samples[0].ffpm }}</td>
-    <td>{{ variant.frame_status }}</td>
-    <td>
-      {% if variant.genes %}
-        {% for gene in variant.genes %}
-          {% for transcript in gene.transcripts %}
-            <div>{{ transcript.transcript_id }} </div>
-          {% endfor %}
-        {% endfor %}
-      {% endif %}
-    </td>
-    <td>
-      {% if variant.genes %}
-        {% for gene in variant.genes %}
-          {% for transcript in gene.transcripts %}
-            <div>{% if "exon" in transcript %}{{ transcript.exon|int }}{% endif %} </div>
-          {% endfor %}
-        {% endfor %}
-      {% endif %}
-    </td>
-    <td> {{ variant.chromosome }}:{{ variant.position }}  <br> {{ variant.end_chrom }}:{{ variant.end }} </td>
-    <td>{{ variant.orientation }}</td>
+    {{ default_fusion_variant_cells(institute, case, variant) }}
   </tr>
 {% endmacro %}
 

scout/server/blueprints/variants/templates/variants/str-variants.html

@@ -91,9 +91,9 @@
 	        {% endif %}
             <td class="str-link">{{ cell_rank(variant, institute, case, form, manual_rank_options) }}</td>
             <td class="str-link">{{ str_locus_info(variant) }}</td>
-	          <td class="text-end">{{ variant.str_display_ru or variant.str_ru  }}</td>
-            <td class="text-end"><b>{{ variant.alternative|replace("STR", "")|replace("<", "")|replace(">", "") }}</b></td>
-            <td class="text-end">{{ variant.str_ref }}</td>
+	          <td class="text-end">{{ variant.str_display_ru or variant.str_ru or variant.reference }}</td>
+            <td class="text-end"><b><span data-bs-toggle="tooltip" title="{{ variant.alternative }}">{{ variant.str_mc }}</span></b></td>
+        <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.reference }}">{{ variant.str_ref or "." }}</span></td>
             <td>{{ str_status(variant) }}</td>
             <td>{% for sample in variant.samples %}
                   {% if sample.genotype_call != "./." %}
@@ -187,7 +187,9 @@
       <tr><td colspan=2>&nbsp;</td></tr>
       {% if variant.str_swegen_mean %}
         <tr><td>SweGen Z-score</td><td>
-          {{ ((variant.alternative|replace("STR", "")|replace("<", "")|replace(">", "")|int - variant.str_swegen_mean ) / variant.str_swegen_std) | round(2) }}
+          {% if variant.str_mc %}
+            {{ ((variant.str_mc - variant.str_swegen_mean ) / variant.str_swegen_std) | round(2) }}
+          {% endif %}
         </td></tr>
         <tr><td>SweGen mean</td><td>{{variant.str_swegen_mean|round(2)}}</td></tr>
         <tr><td>SweGen std</td><td>{{variant.str_swegen_std|round(2)}}</td></tr>
@@ -233,7 +235,8 @@
       {% endfor %}
     {%endif%}
   </div>"
-  title="">{{ variant.str_repid }}
+  title="">{% if variant.str_repid %} {{ variant.str_repid }} {% elif variant.str_trid %} {{ variant.str_trid  }} {% else %}
+  {% for gene in variant.genes %} {{ gene.symbol }} {% endfor %} {% endif %}
   </a>
   {% for gene in variant.genes %}
     <span class="badge bg-secondary"><a href="{{ gene.stripy_link }}" class="text-white" referrerpolicy="no-referrer" rel="noopener" target="_blank">S</a></span>