scout-browser 4.92__py3-none-any.whl → 4.94__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scout/adapter/mongo/base.py +3 -0
- scout/adapter/mongo/case.py +27 -2
- scout/adapter/mongo/ccv.py +131 -0
- scout/adapter/mongo/query.py +88 -53
- scout/adapter/mongo/variant.py +6 -5
- scout/adapter/mongo/variant_events.py +45 -1
- scout/build/ccv.py +59 -0
- scout/commands/export/export_command.py +0 -0
- scout/commands/load/base.py +0 -0
- scout/commands/load/user.py +0 -0
- scout/commands/serve.py +2 -1
- scout/commands/update/disease.py +0 -0
- scout/commands/update/genes.py +0 -0
- scout/commands/wipe_database.py +0 -0
- scout/constants/__init__.py +2 -0
- scout/constants/case_tags.py +2 -0
- scout/constants/ccv.py +244 -0
- scout/demo/643594.config.yaml +2 -2
- scout/demo/images/custom_images/1300x1000.jpg +0 -0
- scout/models/ccv_evaluation.py +26 -0
- scout/models/variant/variant.py +1 -0
- scout/parse/variant/compound.py +0 -0
- scout/parse/variant/gene.py +0 -0
- scout/parse/variant/genotype.py +0 -0
- scout/resources/custom_igv_tracks/mane.bb +0 -0
- scout/server/blueprints/cases/controllers.py +21 -0
- scout/server/blueprints/cases/templates/cases/case_report.html +53 -0
- scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +2 -2
- scout/server/blueprints/cases/templates/cases/index.html +0 -2
- scout/server/blueprints/clinvar/controllers.py +4 -5
- scout/server/blueprints/institutes/controllers.py +129 -67
- scout/server/blueprints/institutes/forms.py +5 -2
- scout/server/blueprints/institutes/templates/overview/cases.html +6 -0
- scout/server/blueprints/institutes/templates/overview/causatives.html +1 -1
- scout/server/blueprints/institutes/templates/overview/utils.html +18 -6
- scout/server/blueprints/institutes/templates/overview/verified.html +1 -1
- scout/server/blueprints/institutes/views.py +4 -0
- scout/server/blueprints/panels/controllers.py +5 -6
- scout/server/blueprints/panels/templates/panels/panel.html +5 -5
- scout/server/blueprints/variant/controllers.py +148 -1
- scout/server/blueprints/variant/templates/variant/cancer-variant.html +1 -1
- scout/server/blueprints/variant/templates/variant/ccv.html +183 -0
- scout/server/blueprints/variant/templates/variant/components.html +61 -3
- scout/server/blueprints/variant/templates/variant/tx_overview.html +3 -3
- scout/server/blueprints/variant/templates/variant/variant.html +1 -1
- scout/server/blueprints/variant/templates/variant/variant_details.html +29 -11
- scout/server/blueprints/variant/utils.py +21 -1
- scout/server/blueprints/variant/views.py +114 -3
- scout/server/blueprints/variants/controllers.py +31 -0
- scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html +4 -18
- scout/server/blueprints/variants/templates/variants/cancer-variants.html +4 -13
- scout/server/blueprints/variants/templates/variants/components.html +77 -73
- scout/server/blueprints/variants/templates/variants/indicators.html +11 -0
- scout/server/blueprints/variants/templates/variants/sv-variants.html +2 -2
- scout/server/links.py +1 -1
- scout/server/static/custom_images.js +19 -2
- scout/utils/acmg.py +0 -1
- scout/utils/ccv.py +201 -0
- scout/utils/md5.py +0 -0
- {scout_browser-4.92.dist-info → scout_browser-4.94.dist-info}/METADATA +67 -45
- {scout_browser-4.92.dist-info → scout_browser-4.94.dist-info}/RECORD +54 -49
- {scout_browser-4.92.dist-info → scout_browser-4.94.dist-info}/WHEEL +1 -2
- scout/__version__.py +0 -1
- scout/demo/images/custom_images/640x480_two.jpg +0 -0
- scout_browser-4.92.dist-info/top_level.txt +0 -1
- {scout_browser-4.92.dist-info → scout_browser-4.94.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.92.dist-info → scout_browser-4.94.dist-info/licenses}/LICENSE +0 -0
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Metadata-Version: 2.
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Metadata-Version: 2.4
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Name: scout-browser
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Version: 4.
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Summary: Clinical DNA variant visualizer and browser
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Version: 4.94
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Summary: Clinical DNA variant visualizer and browser
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Project-URL: Repository, https://github.com/Clinical-Genomics/scout
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Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
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Project-URL: Documentation, https://clinical-genomics.github.io/scout/
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Project-URL: Bug Tracker, https://github.com/Clinical-Genomics/scout/issues
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Project-URL: Issues, https://github.com/Clinical-Genomics/scout/issues
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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>
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License: MIT License
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License-File: LICENSE
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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
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Classifier: Development Status :: 5 - Production/Stable
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Classifier: Environment :: Web Environment
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Classifier: Intended Audience :: Developers
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: MacOS :: MacOS X
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Classifier: Operating System :: Unix
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Classifier: Programming Language :: Python
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Programming Language :: Python :: Implementation :: CPython
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Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
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Requires-Python: >=3.9
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<p align="center">
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<a href="https://Clinical-Genomics.github.io/scout/">
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pip install --editable .
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```
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Scout is configured to use `uv` if you like; either run, install, install as a tool or
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```
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uv sync --frozen
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uv run scout
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```
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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).
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<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/).
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scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
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scout/__version__.py,sha256=ANcNj-w6TB4wETdZ9CZJYc1ZGU2Q1cA11Hzzi92m9BE,21
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scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
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scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
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scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
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scout/adapter/mongo/acmg.py,sha256=v2Zuw-6APVmcnBnNXa18WJEu2vj5GUhZNiKMkruJsBI,4170
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scout/adapter/mongo/base.py,sha256=
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scout/adapter/mongo/case.py,sha256=
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scout/adapter/mongo/base.py,sha256=iIa2AjGNztKHcZzolY0T6r7Oh0guj6R1putztp4OTNY,4427
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scout/adapter/mongo/case.py,sha256=aHHCOeB1wjEX98HKBpDFWC0zZ149Orn93XkW0m7Wj7A,65148
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scout/adapter/mongo/case_events.py,sha256=slHR4XJF9vRuEbuInJKMMAImLF8m7tHWVfGP42fbXr0,26859
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scout/adapter/mongo/case_group.py,sha256=tG8DuO0rNYepV4k0yCGPqssODErc0HMsAypg3mfhcV0,1575
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scout/adapter/mongo/ccv.py,sha256=VIz-Yqzm-1UVPDKvZkBllO4BOKXzvKCXcQUjTtZCHTI,4165
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scout/adapter/mongo/clinvar.py,sha256=tczC39O3DFDkYgjt2RDgkkG-x1Mvx_99Hw7dAbIQ5gk,19838
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scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7uQ,2622
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scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
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scout/adapter/mongo/omics_variant.py,sha256=VdkNG_l6vcr3UF25EixEfvIdMGkSGeNaMjLRhQHS_lc,7521
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scout/adapter/mongo/panel.py,sha256=d1oMEYAiDGybLmlbbf3-fQdCdU0-T7x2XdIUwZGthYk,20031
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scout/adapter/mongo/phenomodel.py,sha256=cypSS8YRzu98Bf1kC0orfrLNn_ZQSYCK8e4mNR5PaPY,2572
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scout/adapter/mongo/query.py,sha256=
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scout/adapter/mongo/query.py,sha256=rF4WjVaH0x1vupJkYMj0c_p8TQbApmZ1t8LgH8MsZwA,34777
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scout/adapter/mongo/rank_model.py,sha256=wvDNI4OLf-f7ZYZ_Q_6qi0myxOJCNNJR_-2-_0u2K2M,5712
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scout/adapter/mongo/transcript.py,sha256=3U1qtyxZ1DnrzdBJm_emJXISMYFKJuX_zAKynUt8NMY,7417
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scout/adapter/mongo/user.py,sha256=QoQnRWqi_dV3ZwGzBonEU6Ap9TgMDf2x_C5UIqG0pa0,2569
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scout/adapter/mongo/variant.py,sha256=
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scout/adapter/mongo/variant_events.py,sha256=
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scout/adapter/mongo/variant.py,sha256=Mwu-2N2ziXSR4lQEFXegbftH2nTskAWL_vpAdeu-i2M,34926
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scout/adapter/mongo/variant_events.py,sha256=yNnMM58P1LbYFw73rWzti6l2zWa_G93ozUTbVkcz4_I,33475
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scout/adapter/mongo/variant_loader.py,sha256=C05StRMFVChopcolPYXFIbh_S-FhYHu4NvBCpiBLOeE,28327
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scout/build/acmg.py,sha256=M21MrrP_dtEyOuu6t-jBDdaqYcHPMLcwJlt9fHG2ycE,1523
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scout/build/case.py,sha256=7Hry6ja0KvVhNQ1ecXy3HuaR7dY2x9O8f8FpYt4P6jo,11404
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scout/build/ccv.py,sha256=cfAWSQ5cSBWURkL9_fPm1Y5aRcTIDOE9ieSWaYLufB4,1660
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scout/build/disease.py,sha256=Zew9AF_z1NbbKcO3uJZ2wgni501SkfnYRgnaCZ4m8FY,2020
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scout/build/hpo.py,sha256=LJBCTq-x09D0CSKcUHB8a6ynuUrVh_7Ia0ooA1BxMys,1207
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scout/build/individual.py,sha256=a2L1NJF11oGaOU9LilWN5gftSyIRfk7H231mF2Y67WU,5232
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scout/commands/view/transcripts.py,sha256=59WyNNp7zHPJIz9QgzrkoeKaSXTtuLli0VuL8IidEmY,1277
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scout/utils/algorithms.py,sha256=w--NauXbQohZis7obr39a8bS57C4NRelYXn79V7m1dU,800
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scout/utils/ccv.py,sha256=85lY7uSjHg3VAfWOfrx9jnaDUQXSa5hDQcRIqZ_Ikas,6025
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scout_browser-4.94.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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scout_browser-4.94.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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