scout-browser 4.93.1__py3-none-any.whl → 4.95.0__py3-none-any.whl

scout/server/blueprints/variants/forms.py

@@ -16,7 +16,7 @@ from wtforms import (
     SubmitField,
     validators,
 )
-from wtforms.widgets import TextInput
+from wtforms.widgets import NumberInput, TextInput
 
 from scout.constants import (
     CALLERS,
@@ -132,8 +132,22 @@ class VariantFiltersForm(FlaskForm):
     )
 
     chrom = NonValidatingSelectMultipleField("Chromosome", choices=[], default="")
-    start = IntegerField("Start position", [validators.Optional()])
-    end = IntegerField("End position", [validators.Optional()])
+    start = IntegerField(
+        "Start position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=0, message="Start position must be 1 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
+    end = IntegerField(
+        "End position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=0, message="End position must be 1 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
     cytoband_start = NonValidatingSelectField("Cytoband start", choices=[])
     cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
 
@@ -264,8 +278,22 @@ class OutlierFiltersForm(FlaskForm):
     )
 
     chrom = NonValidatingSelectMultipleField("Chromosome", choices=[], default="")
-    start = IntegerField("Start position", [validators.Optional()])
-    end = IntegerField("End position", [validators.Optional()])
+    start = IntegerField(
+        "Start position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=1, message="Start position must be 0 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
+    end = IntegerField(
+        "End position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=1, message="End position must be 0 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
     cytoband_start = NonValidatingSelectField("Cytoband start", choices=[])
     cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
 

scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import cancer_sv_filters,cell_rank, pagination_footer, pagination_hidden_div, filter_form_footer, filter_script_main, update_stash_filter_button_status, dismiss_variants_block, callers_cell %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
+{% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - SV variants
@@ -111,8 +111,8 @@
       {{ variant.sub_category|upper }}
     </td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
-    <td class="col-2"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
-    <td class="col-2"><span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
+    <td class="col-2">{% if variant.chromosome != variant.end_chrom %}<span class="text-body"></span><b>{{ variant.chromosome }}</b>:</span>{% endif %}<span class="text-body" style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
+    <td class="col-2">{% if variant.chromosome != variant.end_chrom %}<span class="text-body"><b>{{ variant.end_chrom }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
     <td class="col-2"><span style="white-space: nowrap;">{{ '-' if variant.length == 100000000000 else variant.length|human_longint|safe }}</span></td>
     <td class="text-end">{{ frequency_cell_general(variant) }}</td>
     <td>{{observed_cell_general(variant)}}</td>
@@ -122,25 +122,11 @@
     <td>
       {{ variant_funct_anno_cell(variant) }}
     </td>
-    <td>{{ allele_cell(variant.tumor or {}) }}{% if variant.somatic_score %}<small class="text-muted">[{{ variant.somatic_score }}]</small>{% endif %}</td>
+    <td>{{ allele_cell(variant.tumor or {}) }}{% if variant.somatic_score %}<small class="text-body" data-bs-toggle="tooltip" data-bs-placement="top" title="SV caller (Manta) somatic score">[{{ variant.somatic_score }}]</small>{% endif %}</td>
     <td>{{ allele_cell(variant.normal or {}) }}</td>
   </tr>
 {% endmacro %}
 
-{% macro allele_cell(allele) %}
-  {% if 'alt_freq' in allele %}
-    {% if allele.alt_freq == -1 %}
-      <span class="text-muted">.</span>
-    {% else %}
-      {{ allele.alt_freq|round(4) }}
-    {% endif %}
-    <br>
-    <small class="text-muted">{% if allele.alt_depth >= 0 %}{{ allele.alt_depth }}{% else %}.{% endif %}|{% if allele.ref_depth >= 0 %}{{ allele.ref_depth }}{% else %}.{% endif %}</small>
-  {% else %}
-    <span class="text-muted">N/A</span>
-  {% endif %}
-{% endmacro %}
-
 
 {% block scripts %}
   {{ super() }}

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

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 
-{% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
+{% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
 {% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
 {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, ccv_evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
 
@@ -175,17 +175,7 @@
 {% endmacro %}
 
 {% macro position_cell(variant) %}
-  {{ variant.chromosome }}<span class="text-muted">:{{ variant.position }}</span>
-{% endmacro %}
-
-{% macro allele_cell(allele) %}
-  {% if 'alt_freq' in allele %}
-    {{ allele.alt_freq|round(4)  }}
-    <br>
-    <small class="text-muted">{{ allele.alt_depth }} | {{ allele.ref_depth }}</small>
-  {% else %}
-    <span class="text-muted">N/A</span>
-  {% endif %}
+  <span class="text-body"><b>{{ variant.chromosome }}</b>:{{ variant.position }}</span>
 {% endmacro %}
 
 {% block scripts %}

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

@@ -211,7 +211,7 @@
         title="Overlapping gene panels"
         data-bs-content="{% for panel in matching_panels %}
           {{ panel.panel_name|safe }}<br>
-        {% endfor %}"
+        {% else %} No ovelapping gene panels {% endfor %}"
       >{{ panel_count }}</a>
     {% endmacro %}
 
@@ -403,3 +403,17 @@
   <script src="https://cdn.datatables.net/1.12.0/js/jquery.dataTables.min.js" integrity="sha512-fu0WiDG5xqtX2iWk7cp17Q9so54SC+5lk/z/glzwlKFdEOwGG6piUseP2Sik9hlvlmyOJ0lKXRSuv1ltdVk9Jg==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
   <script src="https://cdn.datatables.net/1.12.0/js/dataTables.bootstrap5.min.js" integrity="sha512-nfoMMJ2SPcUdaoGdaRVA1XZpBVyDGhKQ/DCedW2k93MTRphPVXgaDoYV1M/AJQLCiw/cl2Nbf9pbISGqIEQRmQ==" referrerpolicy="no-referrer" crossorigin="anonymous"></script>
 {% endmacro %}
+
+{% macro allele_cell(allele) %}
+  {% if 'alt_freq' in allele %}
+    {% if allele.alt_freq == -1 %}
+      <span class="text-body">.</span>
+    {% else %}
+      <span class="text-body"><b>{{ allele.alt_freq|round(4) }}</b></span>
+    {% endif %}
+    <br>
+    <small class="text-body">{% if 'alt_depth' in allele and allele.alt_depth >= 0 %}{{ allele.alt_depth }}{% else %}.{% endif %}|{% if 'ref_depth' in allele and allele.ref_depth >= 0 %}{{ allele.ref_depth }}{% else %}.{% endif %}</small>
+  {% else %}
+    <span class="text-body">N/A</span>
+  {% endif %}
+{% endmacro %}

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

@@ -108,8 +108,8 @@ onsubmit="return validateForm()">
     </td>
     <td>{{ variant.sub_category|upper }}</td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
-    <td><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
-<td><span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
+    <td>{% if variant.chromosome != variant.end_chrom %}<span class="text-body"></span><b>{{ variant.chromosome }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
+    <td>{% if variant.chromosome != variant.end_chrom %}<span class="text-body"><b>{{ variant.end_chrom }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
     <td class="text-end"><span style="white-space: nowrap;">{{ '-' if variant.length == 100000000000 else variant.length|human_longint|safe}}</span></td>
     <td>
       {{ frequency_cell_general(variant) }}

scout/server/links.py

@@ -714,7 +714,7 @@ def ucsc_link(variant_obj, build=None):
     )
     if build == 38:
         url_template = (
-            "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg20&"
+            "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&"
             "position=chr{this[chromosome]}:{this[position]}"
             "-{this[position]}&dgv=pack&knownGene=pack&omimGene=pack"
         )

scout/utils/acmg.py

@@ -1,6 +1,5 @@
 # coding=UTF-8
 
-
 from typing import Optional
 
 from scout.constants import ACMG_COMPLETE_MAP

scout/utils/ccv.py

@@ -146,15 +146,7 @@ def get_ccv_temperature(ccv_terms: set) -> Optional[dict]:
     }
 
     if not ccv_terms:
-        points = 0
-        point_classification = "uncertain_significance"
-        return {
-            "points": points,
-            "temperature": TEMPERATURE_STRINGS[points].get("label"),
-            "temperature_class": TEMPERATURE_STRINGS[points].get("color"),
-            "temperature_icon": TEMPERATURE_STRINGS[points].get("icon"),
-            "point_classification": CCV_COMPLETE_MAP[point_classification].get("short"),
-        }
+        return {}
 
     points = get_ccv_points(ccv_terms)
 

scout/utils/link.py

@@ -36,15 +36,16 @@ def genes_by_alias(hgnc_genes):
         hgnc_symbol = gene["hgnc_symbol"]
 
         for alias in gene["previous_symbols"]:
+            alias = alias.upper()
             true_id = None
             if alias == hgnc_symbol:
                 true_id = hgnc_id
             if alias in alias_genes:
-                alias_genes[alias.upper()]["ids"].add(hgnc_id)
+                alias_genes[alias]["ids"].add(hgnc_id)
                 if true_id:
-                    alias_genes[alias.upper()]["true"] = hgnc_id
+                    alias_genes[alias]["true"] = hgnc_id
             else:
-                alias_genes[alias.upper()] = {"true": true_id, "ids": set([hgnc_id])}
+                alias_genes[alias] = {"true": true_id, "ids": set([hgnc_id])}
 
     return alias_genes
 

{scout_browser-4.93.1.dist-info → scout_browser-4.95.0.dist-info}/METADATA

@@ -1,62 +1,76 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.93.1
-Summary: Clinical DNA variant visualizer and browser.
-Home-page: https://github.com/Clinical-Genomics/scout
-Author: Måns Magnusson
-Author-email: mans.magnusson@scilifelab.se
+Version: 4.95.0
+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
+Project-URL: Documentation, https://clinical-genomics.github.io/scout/
+Project-URL: Bug Tracker, https://github.com/Clinical-Genomics/scout/issues
+Project-URL: Issues, https://github.com/Clinical-Genomics/scout/issues
+Author-email: Chiara Rasi <chiara.rasi@scilifelab.se>, Daniel Nilsson <daniel.nilsson@ki.se>, Robin Andeer <robin.andeer@gmail.com>, Mans Magnuson <monsunas@gmail.com>
+License: MIT License
+License-File: LICENSE
+Keywords: acmg,beacon,cancer,clingen-cgc-vicc,clinvar,cnv,coverage,dna,fusion,genome visualisation,lrs,matchmaker exchange,ogm,outliers,panel,panelapp,phenopacket,rna,sma,snv,str,sv,variant ranking,variant triage,variants,vcf,wes,wgs,wts
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Web Environment
 Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Unix
 Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Programming Language :: Python :: 3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: werkzeug
-Requires-Dist: Flask>=2.0
-Requires-Dist: Flask-Bootstrap
-Requires-Dist: Flask-CORS
-Requires-Dist: path.py
-Requires-Dist: markdown
-Requires-Dist: WTForms
-Requires-Dist: Flask-WTF
-Requires-Dist: Flask-Mail
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Requires-Dist: anytree
+Requires-Dist: authlib
+Requires-Dist: cairosvg
+Requires-Dist: click
 Requires-Dist: coloredlogs
-Requires-Dist: query_phenomizer
-Requires-Dist: Flask-Babel>=3
+Requires-Dist: configobj
+Requires-Dist: cryptography
+Requires-Dist: cyvcf2
+Requires-Dist: defusedxml
+Requires-Dist: flask-babel>=3
+Requires-Dist: flask-bootstrap
+Requires-Dist: flask-cors
+Requires-Dist: flask-ldapconn
+Requires-Dist: flask-login
+Requires-Dist: flask-mail
+Requires-Dist: flask-wtf
+Requires-Dist: flask>=2.0
+Requires-Dist: importlib-resources
+Requires-Dist: intervaltree==3.0.2
 Requires-Dist: livereload>=2.7
-Requires-Dist: tornado>=6.4.1
-Requires-Dist: python-dateutil
-Requires-Dist: pymongo
+Requires-Dist: markdown
+Requires-Dist: path-py
 Requires-Dist: pathlib
 Requires-Dist: pdfkit
+Requires-Dist: ped-parser
 Requires-Dist: phenopackets
-Requires-Dist: xlsxwriter
-Requires-Dist: click
-Requires-Dist: cryptography
-Requires-Dist: defusedxml
-Requires-Dist: svglib
-Requires-Dist: cairosvg
-Requires-Dist: importlib_resources
-Requires-Dist: authlib
-Requires-Dist: flask_login
-Requires-Dist: flask-ldapconn
-Requires-Dist: cyvcf2
-Requires-Dist: configobj
-Requires-Dist: ped_parser
 Requires-Dist: pydantic>=2
-Requires-Dist: PyYaml>=5.1
-Requires-Dist: intervaltree==3.0.2
-Requires-Dist: anytree
+Requires-Dist: pymongo
 Requires-Dist: python-dateutil
+Requires-Dist: pyyaml>=5.1
+Requires-Dist: query-phenomizer
+Requires-Dist: svglib
 Requires-Dist: tabulate
+Requires-Dist: tornado>=6.4.1
+Requires-Dist: werkzeug
+Requires-Dist: wtforms
+Requires-Dist: xlsxwriter
 Provides-Extra: coverage
-Requires-Dist: chanjo-report; extra == "coverage"
-Requires-Dist: pymysql; extra == "coverage"
-
+Requires-Dist: chanjo-report; extra == 'coverage'
+Requires-Dist: pymysql; extra == 'coverage'
+Requires-Dist: python-dateutil; extra == 'coverage'
+Description-Content-Type: text/markdown
 
 <p align="center">
 	<a href="https://Clinical-Genomics.github.io/scout/">
@@ -127,6 +141,13 @@ cd scout
 pip install --editable .
 ```
 
+Scout is configured to use `uv` if you like; either run, install, install as a tool or
+```
+uv sync --frozen
+uv run scout
+```
+
+
 Scout PDF reports are created using [Flask-WeasyPrint](https://pythonhosted.org/Flask-WeasyPrint/). This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation [pages](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html#installation).
 
 <b>NB</b>: in order to convert HTML reports into PDF reports, we have recently switched from the WeasyPrint lib to [python-pdfkit](https://github.com/JazzCore/python-pdfkit). For this reason, when upgrading to a Scout version >4.47, you need to install an additional [wkhtmltopdf system library](https://wkhtmltopdf.org/).