TSUMUGI 1.0.1__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.
Files changed (64) hide show
  1. TSUMUGI/annotator.py +103 -0
  2. TSUMUGI/argparser.py +599 -0
  3. TSUMUGI/core.py +185 -0
  4. TSUMUGI/data/impc_phenodigm.csv +3406 -0
  5. TSUMUGI/data/mp.obo +143993 -0
  6. TSUMUGI/filterer.py +36 -0
  7. TSUMUGI/formatter.py +122 -0
  8. TSUMUGI/genewise_annotation_builder.py +94 -0
  9. TSUMUGI/io_handler.py +189 -0
  10. TSUMUGI/main.py +300 -0
  11. TSUMUGI/network_constructor.py +603 -0
  12. TSUMUGI/ontology_handler.py +62 -0
  13. TSUMUGI/pairwise_similarity_builder.py +66 -0
  14. TSUMUGI/report_generator.py +122 -0
  15. TSUMUGI/similarity_calculator.py +498 -0
  16. TSUMUGI/subcommands/count_filterer.py +47 -0
  17. TSUMUGI/subcommands/genes_filterer.py +89 -0
  18. TSUMUGI/subcommands/graphml_builder.py +158 -0
  19. TSUMUGI/subcommands/life_stage_filterer.py +48 -0
  20. TSUMUGI/subcommands/mp_filterer.py +142 -0
  21. TSUMUGI/subcommands/score_filterer.py +22 -0
  22. TSUMUGI/subcommands/sex_filterer.py +48 -0
  23. TSUMUGI/subcommands/webapp_builder.py +358 -0
  24. TSUMUGI/subcommands/zygosity_filterer.py +48 -0
  25. TSUMUGI/validator.py +65 -0
  26. TSUMUGI/web/app/css/app.css +1129 -0
  27. TSUMUGI/web/app/genelist/network_genelist.html +339 -0
  28. TSUMUGI/web/app/genelist/network_genelist.js +421 -0
  29. TSUMUGI/web/app/js/data/dataLoader.js +41 -0
  30. TSUMUGI/web/app/js/export/graphExporter.js +214 -0
  31. TSUMUGI/web/app/js/graph/centrality.js +495 -0
  32. TSUMUGI/web/app/js/graph/components.js +30 -0
  33. TSUMUGI/web/app/js/graph/filters.js +158 -0
  34. TSUMUGI/web/app/js/graph/highlighter.js +52 -0
  35. TSUMUGI/web/app/js/graph/layoutController.js +454 -0
  36. TSUMUGI/web/app/js/graph/valueScaler.js +43 -0
  37. TSUMUGI/web/app/js/search/geneSearcher.js +93 -0
  38. TSUMUGI/web/app/js/search/phenotypeSearcher.js +292 -0
  39. TSUMUGI/web/app/js/ui/dynamicFontSize.js +30 -0
  40. TSUMUGI/web/app/js/ui/mobilePanel.js +77 -0
  41. TSUMUGI/web/app/js/ui/slider.js +22 -0
  42. TSUMUGI/web/app/js/ui/tooltips.js +514 -0
  43. TSUMUGI/web/app/js/viewer/pageSetup.js +217 -0
  44. TSUMUGI/web/app/viewer.html +515 -0
  45. TSUMUGI/web/app/viewer.js +1593 -0
  46. TSUMUGI/web/css/sanitize.css +363 -0
  47. TSUMUGI/web/css/top.css +391 -0
  48. TSUMUGI/web/image/tsumugi-favicon.ico +0 -0
  49. TSUMUGI/web/image/tsumugi-icon.png +0 -0
  50. TSUMUGI/web/image/tsumugi-logo.png +0 -0
  51. TSUMUGI/web/image/tsumugi-logo.svg +69 -0
  52. TSUMUGI/web/js/genelist_formatter.js +123 -0
  53. TSUMUGI/web/js/top.js +338 -0
  54. TSUMUGI/web/open_webapp_linux.sh +25 -0
  55. TSUMUGI/web/open_webapp_mac.command +25 -0
  56. TSUMUGI/web/open_webapp_windows.bat +37 -0
  57. TSUMUGI/web/serve_index.py +110 -0
  58. TSUMUGI/web/template/template_index.html +197 -0
  59. TSUMUGI/web_deployer.py +150 -0
  60. tsumugi-1.0.1.dist-info/METADATA +504 -0
  61. tsumugi-1.0.1.dist-info/RECORD +64 -0
  62. tsumugi-1.0.1.dist-info/WHEEL +4 -0
  63. tsumugi-1.0.1.dist-info/entry_points.txt +3 -0
  64. tsumugi-1.0.1.dist-info/licenses/LICENSE +21 -0
TSUMUGI/web/app/viewer.html ADDED
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+ <!doctype html>
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+ <html lang="en">
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+
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+ <head>
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+ <meta charset="UTF-8" />
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
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+ <title>TSUMUGI Viewer</title>
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+ <link rel="icon" href="../image/tsumugi-favicon.ico" />
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+
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+ <!-- ============================= -->
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+ <!-- JS -->
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+ <!-- ============================= -->
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+ <!-- noUiSlider -->
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+ <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/noUiSlider/15.8.1/nouislider.min.css" />
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+ <script src="https://cdnjs.cloudflare.com/ajax/libs/noUiSlider/15.8.1/nouislider.min.js" defer></script>
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+
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+ <!-- pako for reading gzip JSON -->
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+ <script src="https://cdnjs.cloudflare.com/ajax/libs/pako/2.1.0/pako.min.js" defer></script>
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+
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+ <!-- Cytoscape -->
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+ <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.30.4/cytoscape.min.js" defer></script>
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+ <script src="https://cdn.jsdelivr.net/npm/cytoscape-svg@0.4.0/cytoscape-svg.min.js" defer></script>
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+
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+ <!-- Custom JS -->
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+ <script type="module" src="./viewer.js"></script>
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+
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+ <!-- ============================= -->
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+ <!-- CSS -->
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+ <!-- ============================= -->
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+ <link rel="stylesheet" href="https://larc-tsukuba.github.io/tsumugi/css/sanitize.css" />
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+ <link href="https://fonts.googleapis.com/css?family=Lato" rel="stylesheet" />
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+ <link href="https://use.fontawesome.com/releases/v6.6.0/css/all.css" rel="stylesheet" />
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+ <link rel="stylesheet" href="./css/app.css" />
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+ </head>
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+
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+ <body>
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+ <header class="header-container">
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+ <button id="menu-toggle" class="menu-toggle-icon">
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+ <i class="fa-solid fa-sliders"></i>
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+ </button>
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+ <h1>
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+ Phenotype-Similarity Gene Network of <br />
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+ <a id="page-title-link" href="#" target="_blank" rel="noreferrer"></a>
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+ </h1>
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+ </header>
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+
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+ <div class="body-container">
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+ <button id="toggle-left-panel" class="panel-toggle-button left-panel-toggle" aria-label="Hide left panel">
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+ <i class="fa-solid fa-chevron-left"></i>
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+ </button>
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+ <button id="toggle-right-panel" class="panel-toggle-button right-panel-toggle" aria-label="Hide right panel">
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+ <i class="fa-solid fa-chevron-right"></i>
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+ </button>
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+ <div class="left-control-panel-container">
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+ <button id="close-panel" class="close-button">✕</button>
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+
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+ <!-- ===================================== -->
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+ <!-- Slider for phenotype metrics -->
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+ <!-- ===================================== -->
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+
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+ <!-- Slider for phenotypes similarity -->
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+ <div class="panel-section">
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+ <div class="panel-title">
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+ <i class="fa-solid fa-sliders"></i>
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+ Phenotypic metrics
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+ <div class="info-tooltip-container">
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+ <div class="info-tooltip-icon">i</div>
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+ <div class="info-tooltip-content">Phenotype severity is not displayed when phenotype evaluation
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+ is
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+ binary (presence/absence).</div>
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+ </div>
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+ </div>
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+
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+ <div class="slider-container">
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+ <div class="label-row">
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+ <span class="control-label">Phenotypes similarity:</span>
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+ </div>
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+ <div class="input-row">
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+ <div class="numeric-inputs" aria-label="Phenotypes similarity range">
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+ <input type="number" id="edge-size-min-input" class="range-input" min="1" max="100" step="1"
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+ aria-label="Phenotypes similarity minimum" />
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+ <span class="range-separator">-</span>
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+ <input type="number" id="edge-size-max-input" class="range-input" min="1" max="100" step="1"
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+ aria-label="Phenotypes similarity maximum" />
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+ </div>
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+ </div>
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+ <div class="slider-element" id="filter-edge-slider"></div>
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+ </div>
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+
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+ <div class="slider-container phenotype-only" id="phenotype-severity-controls">
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+ <div class="label-row">
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+ <span class="control-label">Phenotype severity:</span>
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+ </div>
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+ <div class="input-row">
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+ <div class="numeric-inputs" aria-label="Phenotype severity range">
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+ <input type="number" id="node-color-min-input" class="range-input" min="1" max="100" step="1"
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+ aria-label="Phenotype severity minimum" />
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+ <span class="range-separator">-</span>
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+ <input type="number" id="node-color-max-input" class="range-input" min="1" max="100" step="1"
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+ aria-label="Phenotype severity maximum" />
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+ </div>
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+ </div>
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+ <div class="slider-element" id="filter-node-slider"></div>
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+ </div>
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+
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+ </div>
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+
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+ <!-- ===================================== -->
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+ <!-- Filter of Genotype / Sex / Life-stage -->
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+ <!-- ===================================== -->
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+ <div class="panel-section">
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+ <div class="panel-title">
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+ <i class="fa-solid fa-dna"></i>
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+ Biological annotations
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+ </div>
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+
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+ <div class="boxed-section">
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+ <span>Genotype</span>
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+ <form id="genotype-filter-form" class="two-column-options">
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+ <div class="option-column">
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="genotype-all" value="All" checked />
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+ <label for="genotype-all">All</label>
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+ </div>
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="homo" value="Homo" />
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+ <label for="homo">Homo</label>
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+ </div>
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+ </div>
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+ <div class="option-column">
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="hetero" value="Hetero" />
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+ <label for="hetero">Hetero</label>
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+ </div>
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="hemi" value="Hemi" />
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+ <label for="hemi">Hemi</label>
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+ </div>
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+ </div>
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+ </form>
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+ </div>
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+
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+ <div class="boxed-section">
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+ <span>Sex</span>
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+ <form id="sex-filter-form" class="two-column-options">
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+ <div class="option-column">
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="sex-all" value="All" checked />
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+ <label for="sex-all">All</label>
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+ </div>
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+ </div>
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+ <div class="option-column">
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="female" value="Female" />
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+ <label for="female">Female</label>
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+ </div>
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="male" value="Male" />
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+ <label for="male">Male</label>
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+ </div>
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+ </div>
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+ </form>
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+ </div>
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+
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+ <div class="boxed-section">
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+ <span>Life stage
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+ <div class="info-tooltip-container">
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+ <div class="info-tooltip-icon">i</div>
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+ <div class="info-tooltip-content">Early: -16w, Interval: 17-48w, Late: 49w-</div>
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+ </div>
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+ </span>
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+ <form id="lifestage-filter-form" class="two-column-options">
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+ <div class="option-column">
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="lifestage-all" value="All" checked />
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+ <label for="lifestage-all">All</label>
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+ </div>
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="embryo" value="Embryo" />
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+ <label for="embryo">Embryo</label>
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+ </div>
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+ </div>
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+ <div class="option-column">
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="early" value="Early" />
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+ <label for="early">Early</label>
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+ </div>
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="interval" value="Interval" />
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+ <label for="interval">Interval</label>
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+ </div>
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="late" value="Late" />
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+ <label for="late">Late</label>
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+ </div>
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+ </div>
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+ </form>
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+ </div>
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+
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+ </div>
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+ </div>
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+
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+
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+ <div class="cy-container">
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+ <div class="cy"></div>
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+ <div class="cy-controls">
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+ <div class="control-group">
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+ <button id="recenter-button" class="recenter-button" aria-label="Recenter network">
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+ <i class="fa-solid fa-crosshairs"></i>
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+ </button>
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+ <div class="info-tooltip-container">
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+ <div class="info-tooltip-icon" aria-label="Tooltip: recenter network">i</div>
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+ <div class="info-tooltip-content">Recenter and fit the current network in view.</div>
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+ </div>
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+ </div>
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+ <div class="control-group">
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+ <button id="arrange-modules-button" class="recenter-button arrange-modules-button"
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+ aria-label="Arrange modules to avoid overlap">
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+ <i class="fa-solid fa-object-group"></i>
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+ </button>
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+ <div class="info-tooltip-container">
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+ <div class="info-tooltip-icon" aria-label="Tooltip: arrange modules">i</div>
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+ <div class="info-tooltip-content">Arrange modules into a grid to avoid overlap and fit on
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+ screen.</div>
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+ </div>
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+ </div>
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+ </div>
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+ <div id="no-nodes-message" class="no-nodes-message" style="display: none;">No Gene Network Found</div>
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+ </div>
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+
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+ <div class="right-control-panel-container">
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+ <div class="panel-section">
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+ <div class="panel-title">
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+ <i class="fa-regular fa-lightbulb"></i>
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+ Highlight
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+ </div>
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+ <div class="boxed-section align-center">
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+ <span> Markup </span>
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+
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+ <!-- Human disease -->
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+ <form id="human-disease-filter-form">
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+ <div class="round-checkbox">
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+ <input type="checkbox" id="disease" value="Disease" />
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+ <label for="disease">Human Disease</label>
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+ <div class="info-tooltip-container">
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+ <div class="info-tooltip-icon">i</div>
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+ <div class="info-tooltip-content">Human Disease annotations use <a
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+ href="https://diseasemodels.research.its.qmul.ac.uk/" target="_blank">IMPC
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+ Disease
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+ Models</a>. Genes associated with human diseases are
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+ highlighted with a red border.</div>
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+ </div>
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+ </div>
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+ </form>
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+
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+ <!-- Phenotype search -->
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+ <div class="search-container">
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+ <i class="fa-solid fa-magnifying-glass"></i>
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+ <input type="text" id="phenotype-search" placeholder="Phenotypes" />
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+ <ul id="phenotype-suggestions" class="suggestions" hidden></ul>
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+ <div class="info-tooltip-container">
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+ <div class="info-tooltip-icon">i</div>
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+ <div class="info-tooltip-content">
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+ Search for phenotypes to highlight. Genes with matching phenotypes are highlighted with
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+ a
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+ blue border.
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+ </div>
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+ </div>
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+ </div>
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+ <div id="selected-phenotypes" class="selected-phenotypes"></div>
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+
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+ <!-- Gene search -->
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+ <div class="search-container">
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+ <i class="fa-solid fa-magnifying-glass"></i>
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+ <input type="text" id="gene-search" placeholder="Gene Symbol">
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+ <ul id="suggestions" class="suggestions" hidden></ul>
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+ </div>
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+ </div>
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+
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+ <!-- ===================================== -->
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+ <!-- Centrality controls -->
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+ <!-- ===================================== -->
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+ <div class="boxed-section">
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+ <span>Centrality
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+ <div class="info-tooltip-container">
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+ <div class="info-tooltip-icon">i</div>
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+ <div class="info-tooltip-content">
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+ 'Normalized' options divide the centrality score by the number of phenotypes
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+ observed in KO mice
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+ </div>
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+ </div>
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+ </span>
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+
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+ <div class="slider-container">
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+ <div class="label-row">
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+ <label for="centrality-type-dropdown" class="control-label">
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+ </label>
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+ </div>
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+ <div>
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+ <select class="exporter" id="centrality-type-dropdown"
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+ onchange="handleCentralityTypeChange(this.value)">
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+ <option value="none">None</option>
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+ <option value="degree">Degree</option>
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+ <option value="betweenness">Betweenness</option>
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+ <option value="normalized_degree" selected>Normalized Degree</option>
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+ <option value="normalized_betweenness">Normalized Betweenness</option>
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+ </select>
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+ </div>
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+ </div>
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+
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+ <div class="slider-container hidden" id="centrality-slider-container">
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+ <div class="label-row">
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+ <span class="control-label">Scale:</span>
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+ <input type="number" id="centrality-scale-input" class="range-input" min="0" max="100"
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+ step="1" aria-label="Centrality scale" />
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+ </div>
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+ <div class="slider-element" id="centrality-scale-slider"></div>
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+ </div>
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+ </div>
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+ </div>
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+ <!-- ===================================== -->
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+ <!-- Cytoscape's visualization setting -->
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+ <!-- ===================================== -->
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+ <div class="panel-section">
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+ <div class="panel-title">
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+ <i class="fa-solid fa-chart-simple"></i>
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+ Visualization
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+ </div>
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+ <div class="boxed-section">
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+ <span>Layout</span>
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+
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+ <div class="slider-container">
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+ <div class="label-row">
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+ <label for="layout-dropdown" class="control-label"></label>
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+ </div>
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+ <div>
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+ <select class="exporter" id="layout-dropdown">
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+ <option value="cose" selected>Cose</option>
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+ <option value="grid">Grid</option>
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+ <option value="random">Random</option>
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+ <option value="concentric">Concentric</option>
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+ <option value="breadthfirst">Breadthfirst</option>
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+ </select>
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+ </div>
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+ </div>
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+ </div>
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+
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+ <div class="boxed-section" id="node-repulsion-box">
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+ <span>Node repulsion</span>
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+ <div class="slider-container" id="node-repulsion-container">
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+ <div class="label-row">
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+ <span class="control-label">Scale:</span>
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+ <input type="number" id="node-repulsion-input" class="range-input" min="1" max="10" step="1"
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+ aria-label="Node repulsion scale" />
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+ </div>
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+ <div class="slider-element" id="nodeRepulsion-slider"></div>
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+ </div>
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+ </div>
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+
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+ <div class="boxed-section">
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+ <span>Size & Width</span>
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+ <div class="slider-container">
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+ <div class="label-row">
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+ <span class="control-label">Font size:</span>
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+ <input type="number" id="font-size-input" class="range-input" min="1" max="50" step="1"
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+ aria-label="Font size" />
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+ </div>
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+ <div class="slider-element" id="font-size-slider"></div>
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+ </div>
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+
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+ <div class="slider-container">
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+ <div class="label-row">
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+ <span class="control-label">Line width:</span>
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+ <input type="number" id="edge-width-input" class="range-input" min="1" max="10" step="1"
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+ aria-label="Line width" />
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+ </div>
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+ <div class="slider-element" id="edge-width-slider"></div>
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+ </div>
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+ </div>
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+ </div>
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+ </div>
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+ </div>
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+
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+ <!-- ===================================== -->
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+ <!-- SVG for phenotypes similarity -->
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+ <!-- ===================================== -->
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+ <div class="phenotype-scale-container">
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+ <div class="phenotype-scale-wrapper">
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+ <div class="edge-scale-container">
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+ <svg viewBox="0 0 400 30" preserveAspectRatio="xMidYMid meet">
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+ <polygon points="0,15 400,0 400,30" style="fill: gray; stroke: none" />
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+ <text x="0" y="25" font-family="Arial" font-size="12px" fill="#333">Few</text>
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+ <text x="370" y="25" font-family="Arial" font-size="12px" fill="#FFF">Many</text>
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+ </svg>
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+ <p class="scale-label">Similarity of accessory phenotypes</p>
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+ </div>
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+
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+ <div class="color-scale-container phenotype-only" id="phenotype-color-scale">
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+ <svg viewBox="0 0 400 30" preserveAspectRatio="xMidYMid meet">
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+ <defs>
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+ <linearGradient id="colorGradient" x1="0%" y1="0%" x2="100%" y2="0%">
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+ <stop offset="0%" style="stop-color: rgb(248, 229, 140); stop-opacity: 1" />
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+ <stop offset="100%" style="stop-color: rgb(255, 140, 0); stop-opacity: 1" />
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+ </linearGradient>
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+ </defs>
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+ <rect x="0" y="0" width="400" height="30" fill="url(#colorGradient)" />
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+ <text x="0" y="25" font-family="Arial" font-size="12px" fill="#000">Low</text>
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+ <text x="370" y="25" font-family="Arial" font-size="12px" fill="#000">High</text>
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+ </svg>
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+ <p class="scale-label">Severity of target phenotype</p>
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+ </div>
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+ </div>
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+ </div>
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+ <!-- ===================================== -->
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+ <!-- Export (Mobile) -->
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+ <!-- ===================================== -->
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+ <div class="mobile-exporter">
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+ <button class="exporter" id="export-png-mobile">
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+ <i class="fa-regular fa-image"></i>
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+ PNG
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+ </button>
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+ <button class="exporter" id="export-jpg-mobile">
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+ <i class="fa-regular fa-image"></i>
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+ JPG
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+ </button>
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+ <button class="exporter" id="export-svg-mobile">
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+ <i class="fa-solid fa-draw-polygon"></i>
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+ SVG
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+ </button>
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+ <button class="exporter" id="export-csv-mobile">
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+ <i class="fa-regular fa-file-lines"></i>
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+ CSV
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+ </button>
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+ <button class="exporter" id="export-graphml-mobile">
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+ <i class="fa-solid fa-project-diagram"></i>
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+ GraphML
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+ </button>
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+ </div>
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+
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+ <!-- ===================================== -->
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+ <!-- Export (Desktop only) -->
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+ <!-- ===================================== -->
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+ <div class="panel-section export-desktop">
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+ <div class="panel-title">
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+ <i class="fa-solid fa-download"></i>
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+ Export
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+ <div class="info-tooltip-container">
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+ <div class="info-tooltip-icon">i</div>
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+ <div class="info-tooltip-content">
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+ GraphML can be used for visualization in other network analysis tools.
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+ </div>
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+ </div>
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+ </div>
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+ <div class="exporter-group">
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+ <button class="exporter" id="export-png">
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+ <i class="fa-regular fa-image"></i>
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+ PNG
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+ </button>
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+ <button class="exporter" id="export-jpg">
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+ <i class="fa-regular fa-image"></i>
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+ JPG
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+ </button>
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+ <button class="exporter" id="export-svg">
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+ <i class="fa-solid fa-draw-polygon"></i>
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+ SVG
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+ </button>
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+ <button class="exporter" id="export-csv">
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+ <i class="fa-regular fa-file-lines"></i>
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+ CSV
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+ </button>
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+ <button class="exporter" id="export-graphml">
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+ <i class="fa-solid fa-project-diagram"></i>
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+ GraphML
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+ </button>
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+ </div>
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+ </div>
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+
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+
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+ <!-- ======================================== -->
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+ <!-- Footer -->
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+ <!-- ======================================== -->
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+ <footer>
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+
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+ <!-- ======================================== -->
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+ <!-- Resources Section -->
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+ <!-- ======================================== -->
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+ <div class="resources-container">
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+ <div class="resource-section">
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+ <div class="resource-buttons">
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+ <a class="resource-btn" href="https://github.com/akikuno/TSUMUGI-dev/blob/main/README.md"
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+ target="_blank">
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+ <i class="fa-regular fa-file-lines"></i> Documentation
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+ </a>
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+ <a class="resource-btn" href="https://forms.gle/TpLeatthUBLN57PU6" target="_blank">
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+ <i class="fa-regular fa-comment-dots"></i> Contact
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+ </a>
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+ </div>
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+ </div>
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+
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+ </div>
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+
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+ <p>TSUMUGI version <span id="tsumugi-version">-</span></p>
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+ <!-- <p><i class="fa-regular fa-newspaper"></i><a href="https://example.com" target="_blank">Article</a> </p>-->
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+ <p>
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+ &copy; 2026
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+ <a href="https://www.md.tsukuba.ac.jp/LabAnimalResCNT/public_E/index.html" target="_blank">Laboratory
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+ Animal
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+ Resource Center, University of Tsukuba</a>
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+ </p>
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+ </footer>
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+
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+ </body>
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+
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+ </html>