XspecT 0.1.3__py3-none-any.whl → 0.2.0__py3-none-any.whl

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Files changed (58) hide show
  1. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/METADATA +23 -29
  2. XspecT-0.2.0.dist-info/RECORD +30 -0
  3. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/WHEEL +1 -1
  4. xspect/definitions.py +42 -0
  5. xspect/download_filters.py +11 -26
  6. xspect/fastapi.py +101 -0
  7. xspect/file_io.py +34 -103
  8. xspect/main.py +70 -66
  9. xspect/model_management.py +88 -0
  10. xspect/models/__init__.py +0 -0
  11. xspect/models/probabilistic_filter_model.py +277 -0
  12. xspect/models/probabilistic_filter_svm_model.py +169 -0
  13. xspect/models/probabilistic_single_filter_model.py +109 -0
  14. xspect/models/result.py +148 -0
  15. xspect/pipeline.py +201 -0
  16. xspect/run.py +38 -0
  17. xspect/train.py +304 -0
  18. xspect/train_filter/create_svm.py +6 -183
  19. xspect/train_filter/extract_and_concatenate.py +117 -121
  20. xspect/train_filter/html_scrap.py +16 -28
  21. xspect/train_filter/ncbi_api/download_assemblies.py +7 -8
  22. xspect/train_filter/ncbi_api/ncbi_assembly_metadata.py +9 -17
  23. xspect/train_filter/ncbi_api/ncbi_children_tree.py +3 -2
  24. xspect/train_filter/ncbi_api/ncbi_taxon_metadata.py +7 -5
  25. XspecT-0.1.3.dist-info/RECORD +0 -49
  26. xspect/BF_v2.py +0 -637
  27. xspect/Bootstrap.py +0 -29
  28. xspect/Classifier.py +0 -142
  29. xspect/OXA_Table.py +0 -53
  30. xspect/WebApp.py +0 -724
  31. xspect/XspecT_mini.py +0 -1363
  32. xspect/XspecT_trainer.py +0 -611
  33. xspect/map_kmers.py +0 -155
  34. xspect/search_filter.py +0 -504
  35. xspect/static/How-To.png +0 -0
  36. xspect/static/Logo.png +0 -0
  37. xspect/static/Logo2.png +0 -0
  38. xspect/static/Workflow_AspecT.png +0 -0
  39. xspect/static/Workflow_ClAssT.png +0 -0
  40. xspect/static/js.js +0 -615
  41. xspect/static/main.css +0 -280
  42. xspect/templates/400.html +0 -64
  43. xspect/templates/401.html +0 -62
  44. xspect/templates/404.html +0 -62
  45. xspect/templates/500.html +0 -62
  46. xspect/templates/about.html +0 -544
  47. xspect/templates/home.html +0 -51
  48. xspect/templates/layoutabout.html +0 -87
  49. xspect/templates/layouthome.html +0 -63
  50. xspect/templates/layoutspecies.html +0 -468
  51. xspect/templates/species.html +0 -33
  52. xspect/train_filter/README_XspecT_Erweiterung.md +0 -119
  53. xspect/train_filter/get_paths.py +0 -35
  54. xspect/train_filter/interface_XspecT.py +0 -204
  55. xspect/train_filter/k_mer_count.py +0 -162
  56. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/LICENSE +0 -0
  57. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/entry_points.txt +0 -0
  58. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/top_level.txt +0 -0
xspect/templates/layoutabout.html DELETED
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- <!DOCTYPE html>
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- <html lang="en">
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- <head>
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- <!-- Required meta tags -->
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- <meta charset="utf-8">
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- <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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-
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- <!-- Bootstrap CSS -->
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- <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-eOJMYsd53ii+scO/bJGFsiCZc+5NDVN2yr8+0RDqr0Ql0h+rP48ckxlpbzKgwra6" crossorigin="anonymous">
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-
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- <!-- Costum stuff from css file -->
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- <link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='main.css') }}">
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-
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-
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- <script src="https://code.jquery.com/jquery-3.6.0.js" integrity="sha256-H+K7U5CnXl1h5ywQfKtSj8PCmoN9aaq30gDh27Xc0jk=" crossorigin="anonymous"></script>
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- <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta1/dist/js/bootstrap.bundle.min.js" integrity="sha384-ygbV9kiqUc6oa4msXn9868pTtWMgiQaeYH7/t7LECLbyPA2x65Kgf80OJFdroafW" crossorigin="anonymous"></script>
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- <script src="/static/js.js"></script>
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-
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- <meta charset="UTF-8">
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- <title> XspecT </title>
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- <link rel="icon" href="data:,">
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- </head>
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- <body>
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-
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- <!-- navbar -->
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- <header class="site-header">
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- <nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
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- <div class="container-fluid">
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- <a class="navbar-brand mr-4" href="/home" style="padding-left: 10px">Home</a>
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- <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
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- <span class="navbar-toggler-icon"></span>
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- </button>
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- <div class="collapse navbar-collapse" id="navbarToggle">
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- <div class="navbar-nav mr-auto">
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- <a class="nav-item nav-link" href="/species">XspecT</a>
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- <a class="nav-item nav-link" href="/about">About</a>
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- </div>
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- </div>
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- </div>
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- </nav>
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- </header>
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-
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- <!-- Sidebar -->
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- <nav id="sidebarMenu" class="collapse d-lg-block sidebar collapse bg-white">
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- <div class="position-sticky">
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- <div class="list-group list-group-flush mx-3 mt-4">
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- <a href="#About" class="list-group-item list-group-item-action py-2 ripple active" aria-current="true">
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- <i class="fas fa-tachometer-alt fa-fw me-3"></i><span>About this project</span>
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- </a>
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- <a href="#XspecT" class="list-group-item list-group-item-action py-2 ripple">
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- <i class="fas fa-chart-area fa-fw me-3"></i><span>XspecT</span>
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- </a>
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- <a href="#ClAssT" class="list-group-item list-group-item-action py-2 ripple">
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- <i class="fas fa-lock fa-fw me-3"></i><span>ClAssT</span></a>
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- <a href="#How-to-use" class="list-group-item list-group-item-action py-2 ripple">
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- <i class="fas fa-chart-line fa-fw me-3"></i><span>How-to-use</span>
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- </a>
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- <a href="#information" class="list-group-item list-group-item-action py-2 ripple">
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- <i class="fas fa-chart-pie fa-fw me-3"></i><span>General information</span>
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- </a>
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-
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- </div>
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- </div>
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- </nav>
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-
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- <!-- variable content -->
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- <main role="main" class="container">
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- {% block content %}{% endblock %}
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- </main>
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- <!-- Optional JavaScript -->
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- <!-- jQuery first, then Popper.js, then Bootstrap JS -->
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- <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
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- <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
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- <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
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-
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- </body>
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- </html>
xspect/templates/layouthome.html DELETED
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- <!DOCTYPE html>
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- <html lang="en">
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- <head>
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- <!-- Required meta tags -->
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- <meta charset="utf-8">
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- <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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-
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- <!-- Bootstrap CSS -->
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- <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-eOJMYsd53ii+scO/bJGFsiCZc+5NDVN2yr8+0RDqr0Ql0h+rP48ckxlpbzKgwra6" crossorigin="anonymous">
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-
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- <!-- Costum stuff from css file -->
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- <link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='main.css') }}">
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-
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- <script src="https://code.jquery.com/jquery-3.6.0.js" integrity="sha256-H+K7U5CnXl1h5ywQfKtSj8PCmoN9aaq30gDh27Xc0jk=" crossorigin="anonymous"></script>
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- <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta1/dist/js/bootstrap.bundle.min.js" integrity="sha384-ygbV9kiqUc6oa4msXn9868pTtWMgiQaeYH7/t7LECLbyPA2x65Kgf80OJFdroafW" crossorigin="anonymous"></script>
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- <script src="/static/js.js"></script>
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- <meta charset="UTF-8">
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- <title> XspecT </title>
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- <link rel="icon" href="data:,">
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- </head>
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- <body>
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-
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- <!-- Sidebar -->
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- <header class="site-header">
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- <nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
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- <div class="container-fluid">
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- <a class="navbar-brand mr-4" href="/home" style="padding-left: 10px">Home</a>
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- <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
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- <span class="navbar-toggler-icon"></span>
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- </button>
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- <div class="collapse navbar-collapse" id="navbarToggle">
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- <div class="navbar-nav mr-auto">
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- <a class="nav-item nav-link" href="/species">XspecT</a>
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- <a class="nav-item nav-link" href="/about">About</a>
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- </div>
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- </div>
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- </div>
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- </nav>
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- </header>
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-
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- <!-- variable content -->
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- <main role="main" class="container-fluid">
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- <div class="row">
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- <div class="col-md-8 mx-auto">
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- {% block content %}{% endblock %}
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- </div>
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- </div>
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- </main>
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- <!-- Optional JavaScript -->
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- <!-- jQuery first, then Popper.js, then Bootstrap JS -->
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- <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
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- <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
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- <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
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-
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- </body>
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- </html>
xspect/templates/layoutspecies.html DELETED
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- <!DOCTYPE html>
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- <html lang="en">
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- <head>
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- <!-- Required meta tags -->
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- <meta charset="utf-8">
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- <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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- <!-- Bootstrap CSS -->
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- <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-eOJMYsd53ii+scO/bJGFsiCZc+5NDVN2yr8+0RDqr0Ql0h+rP48ckxlpbzKgwra6" crossorigin="anonymous">
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- <!-- Costum stuff from css file -->
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- <link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='main.css') }}">
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- <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
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- <script src="https://code.jquery.com/jquery-3.6.0.js" integrity="sha256-H+K7U5CnXl1h5ywQfKtSj8PCmoN9aaq30gDh27Xc0jk=" crossorigin="anonymous"></script>
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- <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta1/dist/js/bootstrap.bundle.min.js" integrity="sha384-ygbV9kiqUc6oa4msXn9868pTtWMgiQaeYH7/t7LECLbyPA2x65Kgf80OJFdroafW" crossorigin="anonymous"></script>
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- <script src="/static/js.js"></script>
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- <meta charset="UTF-8">
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- <title> XspecT </title>
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- <link rel="icon" href="data:,">
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- </head>
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- <body>
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-
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- <!-- Sidebar -->
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- <div id="content">
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- <header class="site-header">
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- <nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
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- <div class="container-fluid">
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- <a class="navbar-brand mr-4" href="/home" style="padding-left: 10px">Home</a>
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- <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
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- <span class="navbar-toggler-icon"></span>
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- </button>
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- <div class="collapse navbar-collapse" id="navbarToggle">
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- <div class="navbar-nav mr-auto">
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- <a class="nav-item nav-link" href="/species">XspecT</a>
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- <a class="nav-item nav-link" href="/about">About</a>
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- </div>
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- </div>
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- </div>
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- </nav>
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- </header>
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-
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- <!-- variable content -->
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- <main role="main" class="container-fluid">
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- <div class="row">
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- <div class="col-md-4">
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- <div class="popup" id="popup-1">
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- <div class="content">
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- <div class="arrow-left"></div>
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- <div class="close-btn" id="close_popup">&times;</div>
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- XspecT is reasy to use! Upload data for a taxonomic assignment.
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- </div>
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- </div>
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- <div class="content-section" >
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- <h4>Select Genus and upload Sequence Reads or a Genome Assembly</h4>
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- <p> </p>
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- <select class="form-select" aria-label="Select Genus" id="genusSelect">
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- <option value="" id="Preselect" selected disabled hidden>Select Genus</option>
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- <option value="Acinetobacter">Acinetobacter</option>
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- </select>
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- <span id="load_BF" class="input-group-addon" style="display:none">
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- <i class="fa fa-refresh fa-spin"></i>
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- </span>
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- <p> </p>
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- <div class="input-group mb-3">
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- <span class="input-group-text">Train new genus</span>
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- <input type="text" class="form-control" id="genus_text">
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- <button class="btn btn-primary" name="train_new_genus" id="train_new_genus">
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- <span id="start_text">start</span>
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- <span id="genus_loader" class="spinner-border spinner-border-sm" role="status" aria-hidden="true" style="display:none"></span>
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- <span id="loading_text" style="display:none">loading...</span>
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- </button>
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- </div>
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- <p> </p>
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- <input class="form-control" type=file id=infile name=file accept=".fq, .fna, .fasta, .fastq">
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- <!--<form method=post enctype=multipart/form-data> -->
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- <p> </p>
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- <form method="post" role="form">
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- <p></p>
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- <div id="opt">
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- <div id="AspecTinput" style="display:none">
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- <label for="reads_max">Number of Reads:</label>
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- <input type="number" id="reads_max" name="reads_max" min="5000" max="10000000" value="5000" step="100">
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- </div>
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- <p></p>
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- <div id="AspecTinput-2" style="display:none">
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- <p><input type="checkbox" name="quick" id="quick" Checked/> Quick-search</p>
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- </div>
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- <div id="AspecTinput-3">
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- <p><input type="checkbox" name="metagenome" id="metagenome"/> Metagenome</p>
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- </div>
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- <div>
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- <input type="checkbox" name="OXA" id="OXA"/> Oxa-Genes <br><br>
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- </div>
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- <div hidden id="AspecTinput-4">
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- <p><input type="checkbox" name="Amplicon" id="Amplicon"/></p>
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- </div>
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- <button class="btn btn-primary" name="submit" id="submitspec">
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- <span id="submit_text">submit</span>
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- <span id="assignment_loader" class="spinner-border spinner-border-sm" role="status" aria-hidden="true" style="display:none"></span>
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- <span id="assignment_text" style="display:none">loading...</span>
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- </button>
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- <p> </p>
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- </div>
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- </form>
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- </div>
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- <div class="content-section">
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- <h3> Taxonomy</h3>
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- <p>
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- <b>Species:</b> {{prediction}} <br>
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- Results will not be saved, download them if needed!
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- </p>
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- <p hidden>
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- <a id="download_data" download='image' class="download-btn">Download Results
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- <i class="fa fa-download"></i>
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- </a>
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- </p>
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- </div>
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- </div>
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- <div class="col-md-8">
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- <div style = "text-align:center;" class="content-section" >
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- <nav>
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- <div class="nav nav-tabs" id="nav-tab" role="tablist">
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- <button class="nav-link active" id="nav-home-tab" data-bs-toggle="tab" data-bs-target="#nav-home" type="button" role="tab" aria-controls="nav-home" aria-selected="true">Species Assignment</button>
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- <button class="nav-link disabled" id="nav-profile-tab" data-bs-toggle="tab" data-bs-target="#nav-profile" type="button" role="tab" aria-controls="nav-profile" aria-selected="false">Strain-Typing</button>
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- <button class="nav-link disabled" id="nav-oxa-tab" data-bs-toggle="tab" data-bs-target="#nav-oxa" type="button" role="tab" aria-controls="nav-oxa" aria-selected="true">Oxa-Genes</button>
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- <button class="nav-link disabled" id="nav-contact-tab" data-bs-toggle="tab" data-bs-target="#nav-contact" type="button" role="tab" aria-controls="nav-contact" aria-selected="false">Literature</button>
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- </div>
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- </nav>
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- <div class="tab-content" id="nav-tabContent">
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- <div class="tab-pane fade show active" id="nav-home" role="tabpanel" aria-labelledby="nav-home-tab">
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- <br>
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- <h4 id="selectedGenusText" style="text-align: center; margin: 0 auto;">Most similar [Select Genus] species</h4>
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- <img id="logo_XspecT" src="{{url_for('static', filename='Logo.png')}}" width="624" height="468" alt="Error: image not availabe"/>
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- <script src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.7.2/Chart.min.js"></script>
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- <div id="plot_XspecT" class="chart-container" style="position: relative; height:65vh; width:63vw;display:none">
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- <canvas id="polar-chart" width="950" height="800"></canvas>
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- <script>
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- var labels = {{ clonetypes|tojson }};
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- var data = {{ results_ct }};
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- var additionalInfo = {{ additional_info|tojson }};
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- var metagenome = {{ metagenome|tojson }};
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-
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- var myChart = new Chart(document.getElementById("polar-chart"), {
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- type: 'radar',
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- data: {
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- labels: labels,
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- datasets: [
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- {
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- label: "Score",
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- borderColor: "rgb(255, 99, 132)",
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- backgroundColor: "rgba(255, 99, 132, 0.5)",
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- scaleStartValue: 0,
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- data: data
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- }
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- ]
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- },
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- options: {
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- legend: {
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- display: false
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- },
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- responsive: true,
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- maintainAspectRatio: false,
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- scale: {
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- ticks: {
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- beginAtZero: true,
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- max: {{ maxi |tojson}},
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- min: 0,
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- //stepSize: 1
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- }
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- },
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- title: {
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- display: false,
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- text: {{text | tojson}},
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- fontSize: 24
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- },
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- tooltips: {
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- displayColors: false,
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- callbacks: {
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- title: function(tooltipItems, data) {
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- if (metagenome === true) {
186
- return null; // Rückgabe von null, um das Titel-Label zu entfernen
187
- } else {
188
- var dataIndex = tooltipItems[0].index;
189
- return data.labels[dataIndex]; // Rückgabe des normalen Titel-Labels
190
- }
191
- },
192
- label: function(tooltipItem, data) {
193
- if (metagenome === true) {
194
- return null; // Rückgabe von null, um den Wert aus dem Tooltip zu entfernen
195
- } else {
196
- var dataIndex = tooltipItem.index;
197
- return "Score: " + data.datasets[0].data[dataIndex]; // Rückgabe des normalen Werts
198
- }
199
- },
200
- afterBody: function(tooltipItems, data) {
201
- if (metagenome === true) {
202
- var dataIndex = tooltipItems[0].index;
203
- var info = additionalInfo[dataIndex];
204
-
205
- // Aufteilen der Informationen in separate Zeilen
206
- var infoLines = info.split("\n");
207
-
208
- var tooltipContent = [];
209
-
210
- // Jede Information als einzelnen String hinzufügen
211
- for (var i = 0; i < infoLines.length; i++) {
212
- tooltipContent.push(infoLines[i]);
213
- }
214
-
215
- return tooltipContent;
216
- }
217
- else {
218
- return null; // Rückgabe von null, wenn die Bedingung nicht erfüllt ist
219
- }
220
- }
221
- }
222
- },
223
- animation: {
224
- onComplete: function() {
225
- this.options.animation.onComplete = null;
226
- var plot_image = myChart.toBase64Image();
227
- document.getElementById("download_plot").href = plot_image;
228
- document.getElementById("download_plot").download = {{prediction | tojson}} + ".png";
229
- }
230
- }
231
- }
232
- });
233
-
234
- </script>
235
- </div>
236
- <br>
237
- <div id="plot_text" style="display: none">
238
- <h5> Assigned species: {{prediction}} </h5>
239
- <br>
240
- <a id="download_plot" download="image" class="download-btn" style="text-decoration: none;">
241
- Download Plot <i class="fa fa-download"></i>
242
- </a>
243
- <br>
244
- <br>
245
- </div>
246
- </div>
247
-
248
- <div class="tab-pane fade" id="nav-profile" role="tabpanel" aria-labelledby="nav-profile-tab">
249
- <br>
250
- <h4 style="text-align:center;" > A. baumannii Sub-Types </h4>
251
- <script src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.7.2/Chart.min.js"></script>
252
- <div class="chart-container" style="position: relative; height:65vh; width:63vw">
253
- <canvas id="polar-chart-claast" width="950" height="500"></canvas>
254
- <script>
255
- var myChart3 = new Chart(document.getElementById("polar-chart-claast"), {
256
- type: 'radar',
257
- data: {
258
- labels: {{ clonetypes_claast|tojson }},
259
- datasets: [
260
- {
261
- label: "Score",
262
- borderColor: "rgb(54, 162, 235",
263
- backgroundColor: "rgb(54, 162, 235, 0.5)",
264
- scaleStartValue: 0,
265
- data: {{results_claast}}
266
- }
267
- ]
268
- },
269
- options: {
270
- legend: {
271
- display: false
272
- },
273
- responsive: true,
274
- maintainAspectRatio: false,
275
- scale: {
276
- ticks: {
277
- beginAtZero: true,
278
- max: {{ maxi |tojson}},
279
- min: 0,
280
- //stepSize: 1
281
- }
282
- },
283
- title: {
284
- display: false,
285
- text: "A. baumannii Sub-Types"
286
- },
287
- animation: {
288
- onComplete: function() {
289
- //this.options.animation.onComplete = null;
290
- var plot_image = myChart3.toBase64Image();
291
- document.getElementById("download_plot_3").href = plot_image;
292
- document.getElementById("download_plot_3").download = {{prediction_claast | tojson}} + ".png";
293
- }
294
- }
295
- }
296
- });
297
- </script>
298
- </div>
299
- <br>
300
- <h5> Sub-Type: {{prediction_claast}} </h5>
301
- <br>
302
-
303
- <a id="download_plot_3" download='image' class="download-btn">Download Plot
304
- <i class="fa fa-download"></i>
305
- </a>
306
- </div>
307
-
308
-
309
-
310
- <div class="tab-pane fade" id="nav-contact" role="tabpanel" aria-labelledby="nav-contact-tab">
311
- <br>
312
- <div class="row">
313
- <div style="text-align:left" class="col-md-10">
314
-
315
- </div>
316
- <div class="col-md-2">
317
- <button class="btn btn-primary" name="Display_options" id ="Display_options">Display options</button>
318
- </div>
319
- </div>
320
- <div class="span4 collapse-group" style="text-align: left">
321
- <div class="popup-2" id="popup-2">
322
- <div class="content-2">
323
- <div class="input-group">
324
- <div class="form-outline">
325
- Sort by:
326
- <select name="sort" id="id_sort" class="form-select" aria-label="Sort by" data-initial-value="relevance" data-skipped-value="none" data-saved-value="relevance">
327
- <option class="sort-option" value="relevance" data-name="sort" selected="">
328
- Best match
329
- </option>
330
- <option class="sort-option" value="date" data-name="sort">
331
- Most recent
332
- </option>
333
- <option class="sort-option" value="pubdate" data-name="sort">
334
- Publication date
335
- </option>
336
- <option class="sort-option" value="fauth" data-name="sort">
337
- First author
338
- </option>
339
- <option class="sort-option" value="jour" data-name="sort">
340
- Journal
341
- </option>
342
- </select>
343
- </div>
344
- </div>
345
- <br>
346
- <div class="input-group">
347
- <div class="form-outline">
348
- Number of papers:
349
- <input type="number" id="literature_max" class="form-control" name="literature_max" min="1" max="20" value="10" step="1">
350
- </div>
351
- </div>
352
- <br>
353
- <button class="btn btn-primary" name="apply" id="apply">apply</button>
354
- </div>
355
- </div>
356
- <div id="tab-3">
357
-
358
- <ol id="literature">
359
- <!-- dynamically generated list element for each paper -->
360
- </ol>
361
- <script type="text/javascript" {{ url_for('static', filename='js.js')}}></script>
362
- <script type="text/javascript">
363
- myVar = myFunc({{literature_all|tojson}})
364
- </script>
365
- </div>
366
- </div>
367
- </div>
368
- <div class="tab-pane fade" id="nav-oxa" role="tabpanel" aria-labelledby="nav-oxa-tab">
369
- <div class="span4 collapse-group" style="text-align: left">
370
- <div class="media-body">
371
- <br>
372
- <h2 style="text-align:center; color:rgb(255, 159, 64)" > beta-lactamase oxacillinase (bla-OXA) genes </h2>
373
- <p> </p>
374
- <h4 style="text-align:center;"> Percentage of found k-meres in the reference-data</h4>
375
- <p style="text-align:center;"> A OXA-Family is most likely seen as present if it passes a threshold of 0.3 .</p>
376
- <div style = "text-align:center;">
377
- <!-- https://tobiasahlin.com/blog/chartjs-charts-to-get-you-started/#4-radar-chart -->
378
- <script src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/4.3.0/chart.min.js"></script>
379
- <canvas id="oxa-chart" width="750" height="375"></canvas>
380
- <script>
381
- // Source:
382
- //https://stackoverflow.com/questions/40254027/horizontal-bar-chart-in-chart-js
383
- var metagenome = {{ metagenome|tojson }};
384
- if (metagenome === true) {
385
- var oxas = {{ oxa_labels|tojson }};
386
- var results_oxa = {{ oxa_data|tojson }};
387
- } else {
388
- var oxas = {{ oxas|tojson }};
389
- var results_oxa = {{ results_oxa|tojson }};
390
- }
391
- var myChart2 = new Chart(document.getElementById("oxa-chart"), {
392
- type: 'bar',
393
- data: {
394
- labels: oxas,
395
- datasets: [
396
- {
397
- label: "percentage of found k-meres in reference-data",
398
- backgroundColor: "rgb(255, 159, 64)",
399
- //hoverBackgroundColor: "rgba(33, 3, 201, 1)",
400
- data: results_oxa,
401
- }
402
- ]
403
- },
404
- options: {
405
- scales: {
406
- xAxes: [{
407
- barPercentage: 0.2,
408
- source: 'data',
409
- autoSkip: false
410
- }],
411
- yAxes: [{
412
- stacked: true,
413
- ticks: {
414
- min: 0,
415
- max: 1,
416
- }
417
- }]
418
- },
419
- animation: {
420
- onComplete: function() {
421
- // this.options.animation.onComplete = null;
422
- var plot_image_oxa = myChart2.toBase64Image();
423
- document.getElementById("download_oxa").href = plot_image_oxa;
424
- }
425
- }
426
- },
427
- });
428
- </script>
429
- </div>
430
- <p> </p>
431
- </div>
432
- </div>
433
- <br>
434
- <a id="download_oxa" download='bla-OXA.png' class="download-btn">Download Plot
435
- <i class="fa fa-download"></i>
436
- </a>
437
- </div>
438
- </div>
439
- </div>
440
- </div>
441
- </div>
442
- </main>
443
- </div>
444
-
445
- <script>
446
- if ({{filename | tojson}} != "filename") {
447
- document.getElementById("plot_XspecT").style.display = "block";
448
- document.getElementById("logo_XspecT").style.display = "none";
449
- document.getElementById("plot_text").style.display = "block";
450
- document.getElementById("popup-1").style.display = "none";
451
- document.getElementById("nav-contact-tab").classList.remove('disabled');
452
- }
453
- if ({{prediction_claast | tojson}} != "n/a") {
454
- document.getElementById("nav-profile-tab").classList.remove('disabled');
455
- }
456
- if ({{oxas | tojson}} != "None") {
457
- document.getElementById("nav-oxa-tab").classList.remove('disabled');
458
- }
459
-
460
- </script>
461
-
462
- <!-- Optional JavaScript -->
463
- <!-- jQuery first, then Popper.js, then Bootstrap JS -->
464
- <script src="https://cdn.jsdelivr.net/npm/popper.js@1.14.7/dist/umd/popper.min.js" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1" crossorigin="anonymous"></script>
465
-
466
-
467
- </body>
468
- </html>
xspect/templates/species.html DELETED
@@ -1,33 +0,0 @@
1
- {% extends "layoutspecies.html" %}
2
- {% block content %}
3
-
4
- <article class="media content-section">
5
- <div class="media-body">
6
-
7
- <h1>Acinetobacter Species Assignment Tool: XspecT</h1>
8
- <br>
9
- <h4> What is XspecT? </h4>
10
- <p> The '<b>Acinetobacter species Assignment Tool</b>' (AspecT) will assign your given sequence-reads or assembled genome to a <em>Acinetobacter</em> species.
11
- If an assignment is not possible, it is not a species of <em>Acinetobacter</em> or not a species currently covered by the tool.
12
- </p>
13
- <h4> How it works </h4>
14
- AspecT uses Bloom Filters to check k-mers from the input-data for exact matches with our database.
15
- It then taxonomically assigns the input-data to the <em>Acinetobacter</em> species with the k-mer most matches.<br> A Support Vector Machine (SVM) further ensures that
16
- closely related species, e.g. species of the <em>A. calcoaceticus-A. baumannii-complex</em> (ACB-complex), will be assigned correctly.<br><br>
17
- <h4> How to use the Tool</h4>
18
- AspecT can take FASTA-files (.fq/.fna) as upload-data for assembled genomes and FASTQ-files (.fq) for sequence-reads.
19
- For sequence-reads you can choose the amount of reads that will be used for the assignment.
20
- 5000 reads are the minimum amount (with 100.000 Reads as maximum) sufficient for the toxonomic assignment.
21
- Using more reads can lead to a more accurate assignment but will take more time. <br><br>
22
- Please note that the tool was designed for high quality sequence-reads <br>(<1% Error-Rate) with a length of 125-250bp for each read (e.g. Illumina-Reads).<br>
23
- An accurate assignment using reads with a high error-rate is not guaranteed.
24
- Please also note that AspecT only requires a small amount of k-mers for the assignment so that not every k-mere from the assembled genome or sequence-read will be used.
25
- If you want to use all k-mers you can disable the quick-search. Beware of runtimes of about <h8 style="color:red;"> ~10 minutes</h8>. <br>
26
- Click <a href="/about"> here </a> for more information on how AspecT performs the toxonomic assignment.
27
-
28
-
29
-
30
- </div>
31
- </article>
32
-
33
- {% endblock content %}