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

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  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/about.html DELETED
@@ -1,544 +0,0 @@
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- {% extends "layoutabout.html" %}
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- {% block content %}
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-
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- <article class="media content-section">
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- <div class="media-body" id="About">
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- <h1> XspecT and ClAssT</h1>
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- <br>
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- <p>
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- The '<b>Acinetobacter species Assignment Tool</b>' (XspecT) and the integrated '<b>Clone-type Assinment Tool</b>'(ClAssT) are both very fast and easy to use tools to taxonomically assign Acinetobacter Input-Data using Bloom Filters.
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- XspecT performs a taxonomic assignment on the Acinetobacter Species-Level while ClAssT uses Strain-Typing to
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- identify International-Clones of A.baumannii.
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- </p>
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- <br>
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- <h2>About Acinetobacter</h2>
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-
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- <p> The genus <a href="https://en.wikipedia.org/wiki/Acinetobacter">Acinetobacter </a> is a ubiquitous and highly divers group of aerobic and gram-negative bacteria consisting of about 94 different species.
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- They occour in many ecological niches such as soil, water and in animals. They are able to survive with limited amounts of nutrients on dry surfaces and transmiss in natural and medical environment.
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- </p>
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- <p> The taxonomic assignment of Acinetobacter species is difficult for several reasons. One of them are high similarities between closely related species.
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- Espacially those of the <em>A. calcoaceticus-A. baumannii-complex</em> (ACB-complex). 5 out of 6 species of the ACB-complex are pathogens that can cause nosocomial infections.
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- Therefore it is important to taxonomically assign Acinetobacter genomes to the correct species.
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- </p>
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- <h2>{{ 'A.baumannii' }}</h2>
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- <p> <a href="https://en.wikipedia.org/wiki/Acinetobacter_baumannii"> Acinetobacter baumannii </a> is a
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- bacterium that can cause nosocomial infections and build up multidrug resistance. Therefore, this
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- organism can be a threat to patients with a weak immune system that are currently in a hospital environment.</p>
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- <p>
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- There are 8 'International Clonetypes' of A.baumannii with different behaviour regarding
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- <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850921/" >virulence or epidemicity. </a> A
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- identification of the present Clonetype is needed to deal with the outbreak. Current methods, like the
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- 'Multi Locus Sequence Typing (MLST)'-method, are very time consuming.
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- </p>
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- <p>
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- To identify a A.baumannii International Clone, we developed the 'Clone-type Assignment Tool (ClAssT)' that can use
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- Sequence-Reads or a assembled genome as Input-data for a fast
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- and accurate classification. The assembling process of sequence reads is also
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- very time consuming, but with this tool it can be skipped. ClAssT only needs a few Sequence-Reads for
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- a classification. To avoid a long upload of a huge file that contains those reads, this tool will read
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- your input-file client-side and then sends the needed data to the server for further processing.
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- </p>
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- </div>
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- </article>
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-
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-
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- <article class="media content-section">
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- <div class="media-body" id="XspecT">
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-
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- <h2>{{ 'About XspecT' }}</h2>
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- <!-- TODO: CHANGE WORDING -->
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- <p> XspecT is similar to ClAssT. For a taxonomic assignment to be performed on the species level the Input-Data is processed with the same File-Reader and the Bloom Filter are
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- searched through the same modules. For each species up to 4 different assembled genomes (if availabe) were used as reference-data for the Bloom Filters.
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- Only a small amount of k-mers are needed for the species assignment. XspecT uses only every 500th k-mere of a assembled genome and only every 10th k-mer of a Sequence-Read.
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- <br> The Support Vector Machine (SVM) was further improved using the radial basis function as kernel-function with a regularization parameter of C = 1.5.
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- </p>
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- <p></p>
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- <p> This tool was tested and evaluated with over 3600 Acinetobacter genomes and reached an high accuracy of 99.52%.
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- Regardless, we do not take over any liability for any false results and classifications.</p>
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- <p> The used code can be found <a href="https://github.com/Dominik0304/AspecT">here</a> on Github. </p>
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- <h4> How it Works </h4>
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- <p> </p>
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- <p style="text-align:center;">
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- <img src="{{ url_for('static', filename='Workflow_AspecT.png') }}" width="423" height="759" alt="Workflow">
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- </p>
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-
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- <br class="clear"/>
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- <h4> Reference-data</h4>
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- <details>
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- <summary> <b> Used reference-data</b></summary>
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- <p> The tool uses a set of up to 4 assemblys for each species. <br>
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- The used Training-Data for the SVM can be found <a href="https://github.com/Dominik0304/AspecT">here</a>.</p>
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- <table>
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- <tr>
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- <th>Species </th>
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- <th style='text-align:center;vertical-align:middle'>NCBI RefSeq Assembly Accession (GCF)</th>
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- </tr>
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- <tr>
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- <td>A. albensis</td>
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- <td>GCF_900095025.1, GCF_015209685.1</td>
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- </tr>
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- <tr>
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- <td>A. apis</td>
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- <td>GCF_900197575.1</td>
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- </tr>
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- <tr>
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- <td>A. baretiae</td>
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- <td>GCF_015627105.1, GCF_015627115.1</td>
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- </tr>
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- <tr>
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- <td>A. baumannii</td>
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- <td>GCF_000453565.1, GCF_000453645.1, GCF_000453665.1, GCF_000453685.1</td>
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- </tr>
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- <tr>
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- <td>A. baylyi</td>
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- <td>GCF_000302115.1, GCF_000368685.1, GCF_000621045.1, GCF_001485005.1</td>
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- </tr>
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- <tr>
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- <td>A. beijerinckii</td>
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- <td>GCF_000368985.1, GCF_000369005.1, GCF_000931715.1</td>
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- </tr>
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- <tr>
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- <td>A. bereziniae</td>
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- <td>GCF_000248295.1, GCF_000368505.1, GCF_001055215.1, GCF_001500155.1</td>
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- </tr>
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- <tr>
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- <td>A. bohemicus</td>
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- <td>GCF_000367925.1, GCF_900116265.1</td>
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- </tr>
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- <tr>
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- <td>A. boissieri</td>
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- <td>GCF_900096955.1</td>
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- </tr>
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- <tr>
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- <td>A. bouvetii</td>
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- <td>GCF_000368865.1, GCF_000373725.1, GCF_001485025.1</td>
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- </tr>
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- <tr>
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- <td>A. brisouii</td>
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- <td>GCF_000368645.1, GCF_000488275.1, GCF_000931655.1, GCF_000964015.1</td>
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- </tr>
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- <tr>
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- <td>A. calcoaceticus</td>
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- <td>GCF_000162035.1, GCF_000818215.1, GCF_000931735.1, GCF_001510805.1</td>
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- </tr>
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- <tr>
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- <td>A. celticus</td>
126
- <td>GCF_001707755.1</td>
127
- </tr>
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- <tr>
129
- <td>A. chengduensis</td>
130
- <td>GCF_003664645.1</td>
131
- </tr>
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- <tr>
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- <td>A. chinensis</td>
134
- <td>GCF_002165375.2</td>
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- </tr>
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- <tr>
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- <td>A. colistiniresistens</td>
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- <td>GCF_000413935.1</td>
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- </tr>
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- <tr>
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- <td>A. courvalinii</td>
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- <td>GCF_000369605.1, GCF_000369785.1, GCF_000580655.1</td>
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- </tr>
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- <tr>
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- <td>A. cumulans</td>
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- <td>GCF_003024525.3, GCF_003611525.1, GCF_003611535.1, GCF_003611575.1</td>
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- </tr>
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- <tr>
149
- <td>A. defluvii</td>
150
- <td>GCF_001704615.1, GCF_013072655.1</td>
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- </tr>
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- <tr>
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- <td>A. dispersus</td>
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- <td>GCF_009884975.1</td>
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- </tr>
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- <tr>
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- <td>A. equi</td>
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- <td>GCF_001307195.1</td>
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- </tr>
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- <tr>
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- <td>A. GS06</td>
162
- <td>GCF_000367985.1, GCF_000369505.1</td>
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- </tr>
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- <tr>
165
- <td>A. GS16</td>
166
- <td>GCF_000764915.1, GCF_000369525.1, GCF_000368445.1</td>
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- </tr>
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- <tr>
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- <td>A. guerrae</td>
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- <td>GCF_003611455.1, GCF_009014115.1, GCF_009372255.1</td>
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- </tr>
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- <tr>
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- <td>A. gandensis</td>
174
- <td>GCF_001678755.1, GCF_008802205.1</td>
175
- </tr>
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- <tr>
177
- <td>A. gerneri</td>
178
- <td>GCF_000368565.1, GCF_000430245.1, GCF_000747725.1</td>
179
- </tr>
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- <tr>
181
- <td>A. guillouiae</td>
182
- <td>GCF_000368485.1, GCF_000414055.1, GCF_000829655.1, GCF_002370525.1</td>
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- </tr>
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- <tr>
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- <td>A. gyllenbergii</td>
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- <td>GCF_000414075.1, GCF_000488195.1, GCF_000931695.1, GCF_001682515.1</td>
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- </tr>
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- <tr>
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- <td>A. haemolyticus</td>
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- <td>GCF_000369085.1, GCF_000430205.1, GCF_000830135.1, GCF_000302315.1</td>
191
- </tr>
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- <tr>
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- <td>A. halotolerans</td>
194
- <td>GCF_004208515.1</td>
195
- </tr>
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- <tr>
197
- <td>A. harbinensis</td>
198
- <td>GCF_000816495.1</td>
199
- </tr>
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- <tr>
201
- <td>A. idrijaensis</td>
202
- <td>GCA_905480265.1</td>
203
- </tr>
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- <tr>
205
- <td>A. indicus</td>
206
- <td>GCF_000488255.1, GCF_000830155.1, GCF_000964095.1, GCF_001922625.1</td>
207
- </tr>
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- <tr>
209
- <td>A. johnsonii</td>
210
- <td>GCF_000302335.1, GCF_000368045.1, GCF_000368805.1, GCF_000949655.1</td>
211
- </tr>
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- <tr>
213
- <td>A. junii</td>
214
- <td>GCF_000368765.1, GCF_000430225.1, GCF_000775815.1, GCF_000813495.1</td>
215
- </tr>
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- <tr>
217
- <td>A. kanungonis</td>
218
- <td>GCF_009939195.1</td>
219
- </tr>
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- <tr>
221
- <td>A. kookii</td>
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- <td>GCF_900096895.1</td>
223
- </tr>
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- <tr>
225
- <td>A. kyonggiensis</td>
226
- <td>GCF_900107285.1</td>
227
- </tr>
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- <tr>
229
- <td>A. lactucae</td>
230
- <td>GCF_001605885.1, GCF_002076935.1, GCF_001595745.1, GCF_013122135.1</td>
231
- </tr>
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- <tr>
233
- <td>A. lanii</td>
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- <td>GCF_011191955.1, GCF_011578285.1</td>
235
- </tr>
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- <tr>
237
- <td>A. larvae</td>
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- <td>GCF_001704115.1</td>
239
- </tr>
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- <tr>
241
- <td>A. lwoffii</td>
242
- <td>GCF_000162095.1, GCF_000248355.1, GCF_000301755.1</td>
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- </tr>
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- <tr>
245
- <td>A. marinus</td>
246
- <td>GCF_900096915.1</td>
247
- </tr>
248
- <tr>
249
- <td>A. modestus</td>
250
- <td>GCF_014636095.1</td>
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- </tr>
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- <tr>
253
- <td>A. nectaris</td>
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- <td>GCF_000488215.1</td>
255
- </tr>
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- <tr>
257
- <td>A. nosocomialis</td>
258
- <td>GCF_000472005.1, GCF_000529215.1, GCF_000775795.1, GCF_000775895.1</td>
259
- </tr>
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- <tr>
261
- <td>A. oleivorans</td>
262
- <td>GCF_000196795.1, GCF_000488235.1, GCF_000836035.1</td>
263
- </tr>
264
- <tr>
265
- <td>A. parvus</td>
266
- <td>GCF_000248155.1, GCF_000368005.1, GCF_000368025.1, GCF_000962795.1</td>
267
- </tr>
268
- <tr>
269
- <td>A. piscicola</td>
270
- <td>GCF_002233755.1, GCF_004152775.1, GCF_015218165.1</td>
271
- </tr>
272
- <tr>
273
- <td>A. pittii</td>
274
- <td>GCF_000949775.1, GCF_000949795.1, GCF_001005885.1, GCF_001056355.1</td>
275
- </tr>
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- <tr>
277
- <td>A. pollinis</td>
278
- <td>GCF_015627175.1, GCF_015627205.1, GCF_015627215.1, GCF_015627235.1</td>
279
- </tr>
280
- <tr>
281
- <td>A. populi</td>
282
- <td>GCF_002174125.1</td>
283
- </tr>
284
- <tr>
285
- <td>A. portensis</td>
286
- <td>GCF_009372215.1, GCF_010646905.1, GCF_001605895.1</td>
287
- </tr>
288
- <tr>
289
- <td>A. proteolyticus</td>
290
- <td>GCF_001753605.1, GCF_002835245.1, GCF_000367945.1</td>
291
- </tr>
292
- <tr>
293
- <td>A. pseudolwoffii</td>
294
- <td>GCF_0003694451.1, GCF_000369105.1</td>
295
- </tr>
296
- <tr>
297
- <td>A. pullicarnis</td>
298
- <td>GCF_006352475.1</td>
299
- </tr>
300
- <tr>
301
- <td>A. puyangensis</td>
302
- <td>GCF_900096995.1</td>
303
- </tr>
304
- <tr>
305
- <td>A. qingfengensis</td>
306
- <td>GCF_001753595.1, GCF_008693185.1</td>
307
- </tr>
308
- <tr>
309
- <td>A. radioresistens</td>
310
- <td>GCF_000368885.1, GCF_000368905.1, GCF_000972345.1, GCF_001917365.1</td>
311
- </tr>
312
- <tr>
313
- <td>A. rathckeae</td>
314
- <td>GCF_015627125.1, GCF_015627165.1</td>
315
- </tr>
316
- <tr>
317
- <td>A. rongchengensis</td>
318
- <td>GCF_003611475.1</td>
319
- </tr>
320
- <tr>
321
- <td>A. rudis</td>
322
- <td>GCF_000413895.1, GCF_000829675.1</td>
323
- </tr>
324
- <tr>
325
- <td>A. schindleri</td>
326
- <td>GCF_000368465.1, GCF_000368625.1, GCF_001485065.1, GCF_001971565.1</td>
327
- </tr>
328
- <tr>
329
- <td>A. seifertii</td>
330
- <td>GCF_000368065.1, GCF_001054375.1, GCF_001707675.1, GCF_002148925.1</td>
331
- </tr>
332
- <tr>
333
- <td>A. seohaensis</td>
334
- <td>GCA_018403785.1</td>
335
- </tr>
336
- <tr>
337
- <td>A. shaoyimingii</td>
338
- <td>GCF_011174715.1, GCF_011578045.1</td>
339
- </tr>
340
- <tr>
341
- <td>A. sichuanensis</td>
342
- <td>GCF_003024515.2</td>
343
- </tr>
344
- <tr>
345
- <td>A. soli</td>
346
- <td>GCF_000368725.1, GCF_000633005.1, GCF_000760595.1, GCF_001414585.1</td>
347
- </tr>
348
- <tr>
349
- <td>A. stercoris</td>
350
- <td>GCF_900323515.1</td>
351
- </tr>
352
- <tr>
353
- <td>A. tandoii</td>
354
- <td>GCF_000400735.1, GCF_000621065.1, GCF_000760555.1</td>
355
- </tr>
356
- <tr>
357
- <td>A. terrae</td>
358
- <td>GCF_001647595.1, GCF_002135195.1, GCF_004331165.1, GCF_013004255.1</td>
359
- </tr>
360
- <tr>
361
- <td>A. terrestris</td>
362
- <td>GCF_004331115.1, GCF_004331155.1, GCF_004331185.1, GCF_013004415.1</td>
363
- </tr>
364
- <tr>
365
- <td>A. tianfuensis</td>
366
- <td>GCF_003611465.1</td>
367
- </tr>
368
- <tr>
369
- <td>A. tjernbergiae</td>
370
- <td>GCF_000374425.1, GCF_000488175.1, GCF_000759995.1</td>
371
- </tr>
372
- <tr>
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- <td>A. towneri</td>
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- <td>GCF_000368785.1, GCF_000688495.1, GCF_000760575.1, GCF_001758345.1</td>
375
- </tr>
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- <tr>
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- <td>A. ursingii</td>
378
- <td>GCF_000368845.1, GCF_000369885.1, GCF_000934145.1, GCF_000949815.1</td>
379
- </tr>
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- <tr>
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- <td>A. variabilis</td>
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- <td>GCF_000369625.1, GCF_000804305.1, GCF_000368385.1, GCF_018409485.1</td>
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- </tr>
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- <tr>
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- <td>A. venetianus</td>
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- <td>GCF_000308235.1, GCF_000368585.1, GCF_001484985.1, GCF_001577485.1</td>
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- </tr>
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- <tr>
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- <td>A. vivianii</td>
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- <td>GCF_014635885.1, GCF_016502725.1</td>
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- </tr>
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- <tr>
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- <td>A. wanghuae</td>
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- <td>GCF_009557235.1, GCF_009601085.1</td>
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- </tr>
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- <tr>
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- <td>A. wuhouensis</td>
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- <td>GCF_001696605.3, GCF_002165345.2, GCF_004209115.1, GCF_004209325.1</td>
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- </tr>
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- </table>
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- </details>
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- </div>
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- </article>
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-
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- <article class="media content-section">
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- <div class="media-body" id="ClAssT">
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-
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- <h2>{{ 'About ClAssT' }}</h2>
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- <p> The code for the assignment process is inspired by <a href="https://github.com/Phelimb/BIGSI"> BIGSI.</a></p>
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- <p> Find the actual used code for this thesis project <a href="https://github.com/w0rt0x/ClAssT---Acinetobacter-baumannii-Clone-type-Assignment-Tool"> here. </a></p>
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- <p> This tool has been evaluated by validating more than 2700 MLST-classifications of Acinetobacter genomes.
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- Regardless, we do not take over any liability for any false results and classifications.</p>
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- <h4> How it Works </h4>
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- <p> </p>
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- <p style="text-align:center;">
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- <img src="{{ url_for('static', filename='Workflow_ClAssT.png') }}" width="900" height="550" alt="Workflow">
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- </p>
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-
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- <br class="clear"/>
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- <h4> Reference-data</h4>
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- <details>
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- <summary> <b> Used reference-data</b></summary>
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- <p> The tool uses a set of Assemblys per Clonetype. </p>
424
- <table>
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- <tr>
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- <th>Clonetype </th>
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- <th style='text-align:center;vertical-align:middle'>NCBI RefSeq Assembly Accession (GCF)</th>
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- </tr>
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- <tr>
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- <td>IC1</td>
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- <td>'GCF_000369185.1', 'GCF_000453105.1', 'GCF_002416345.1', 'GCF_000177695.1',
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- 'GCF_001444225.1', 'GCF_001657725.1', 'GCF_900031715.1', 'GCF_002119355.1',
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- 'GCF_000309275.1', 'GCF_000453045.1', 'GCF_000586635.1', 'GCF_001444255.1',
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- 'GCF_001399655.1', 'GCF_000969385.1'</td>
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- </tr>
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- <tr>
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- <td>IC2</td>
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- <td>'GCF_000809645.3', 'GCF_002762155.1', 'GCF_000580275.1', 'GCF_000810425.3',
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- 'GCF_000589595.1', 'GCF_000309175.1', 'GCF_002183905.1', 'GCF_000811545.3',
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- 'GCF_001669115.1', 'GCF_000939555.2', 'GCF_002277385.1', 'GCF_002183625.1',
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- 'GCF_900118135.1', 'GCF_001433675.1'</td>
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- </tr>
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- <tr>
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- <td>IC3</td>
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- <td>'GCF_000309215.1', 'GCF_001950095.1', 'GCF_002136595.1', 'GCF_001950315.1',
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- 'GCF_001432825.1', 'GCF_000286535.1', 'GCF_000305295.1', 'GCF_001666225.1',
447
- 'GCF_002016825.1', 'GCF_000215005.1', 'GCF_000581435.1', 'GCF_000278645.1',
448
- 'GCF_000278625.1', 'GCF_002150405.1'</td>
449
- </tr>
450
- <tr>
451
- <td>IC4</td>
452
- <td>'GCF_000368245.1', 'GCF_000988155.1', 'GCF_001500225.1', 'GCF_001758085.1',
453
- 'BMBF-193'</td>
454
- </tr>
455
- <tr>
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- <td>IC5</td>
457
- <td>'GCF_001433245.1', 'GCF_001433015.1', 'GCF_001414735.1', 'GCF_002143145.1',
458
- 'GCF_000302255.1', 'GCF_001415385.1', 'GCF_000515855.1', 'GCF_002137495.1',
459
- 'GCF_002018995.1', 'GCF_002183505.1', 'GCF_001649805.1', 'GCF_001432975.1',
460
- 'GCF_001649795.1', 'GCF_001433655.1'</td>
461
- </tr>
462
- <tr>
463
- <td>IC6</td>
464
- <td>'GCF_000453985.1', 'GCF_900161935.1', 'GCF_001432845.1', 'GCF_900161985.1',
465
- 'GCF_900161915.1', 'GCF_000189695.1', 'GCF_000453965.1', 'GCF_900161995.1',
466
- 'GCF_000681555.1', 'GCF_000516155.1', 'GCF_900161975.1', 'GCF_900161955.1',
467
- 'GCF_900162015.1', 'GCF_900161885.1'</td>
468
- </tr>
469
- <tr>
470
- <td>IC7</td>
471
- <td>'GCF_002573805.1', 'GCF_001007725.1', 'GCF_001612105.1', 'GCF_001007705.1',
472
- 'GCF_001611995.1', 'GCF_000583375.1', 'GCF_002573915.1', 'GCF_000278665.1',
473
- 'GCF_000241705.1', 'GCF_001612095.1', 'GCF_002143975.1', 'GCF_002927855.1',
474
- 'GCF_000516575.2', 'GCF_002504145.1'</td>
475
- </tr>
476
- <tr>
477
- <td>IC8</td>
478
- <td>'GCF_002137755.1', 'GCF_001864715.1', 'GCF_002573795.1', 'GCF_001441455.1',
479
- 'GCF_002017485.1', 'GCF_000588675.1', 'GCF_001441415.1', 'GCF_001441565.1',
480
- 'GCF_001861935.1', 'GCF_002183925.1', 'GCF_001578145.1', 'GCF_001441405.1',
481
- 'GCF_001908295.1', 'GCF_002144965.1'</td>
482
- </tr>
483
- </table>
484
- </details>
485
- <details>
486
- <summary><b> Classification with Support Vector Machine</b></summary>
487
- <p> The tool generates a vector, each vector element holds the score of a selected filter. To assign the
488
- result vector to one of the selected organisms (or none of them), a Machine Learning method called
489
- 'Support Vector Machine (SVM)' has been used. SVM needs training-data for classification, the following
490
- vectors have been used as training-data for your assignment: </p>
491
- <!-- Sources for table -->
492
- <!-- https://sarahleejane.github.io/learning/python/2015/08/09/simple-tables-in-webapps-using-flask-and-pandas-with-python.html -->
493
- <!-- https://stackoverflow.com/questions/52019676/dynamic-table-with-python/52026920 -->
494
- <div style = "text-align:center;" >
495
- {{ svm_table | safe }}
496
- </div>
497
- </details>
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- <details>
499
- <summary> <b> bla-OXA-genes</b></summary>
500
- <p> The following bla-OXA-Families are currently available:</p>
501
- {% for id in oxa_ids%}
502
- <p>{{ id }} </p>
503
- {% endfor %}
504
- </details>
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- </div>
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- </article>
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-
508
-
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- <article class="media content-section">
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- <div class="media-body" id="How-to-use">
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- <h2> How-to-use</h2>
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- <br>
513
- <p style="text-align:center;">
514
- <img src="{{ url_for('static', filename='How-to.png') }}" width="1200" height="600" alt="Workflow">
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- </p>
516
- <ol>
517
- <li> Select your sequence reads or assembled genome input-data. Allowed formats are fna/fasta and fastq <br>
518
- Adjust options: Oxa-Genes = Screen for Oxa-families, Quick-Mode (only for fna/fasta) = fast search, takes less k-mers (default mode)
519
- Sequence-Reads = Amount of reads that will be used (5000 at default). <br>
520
- </li>
521
- <li> The result of the taxonomic assignment will be shown here.</li>
522
- <li> A detailed results plot for the species assignment/strain-typing will be shown here.<br>
523
- The other tabs include a plot for all oxa.genes (if the option was selected), and a literature search with relevant papers from PubMed to the assigned species. <br>
524
- All plots can be downloaded with the download-button at the bottom of each plot.</li>
525
- </ol>
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- </div>
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- </article>
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-
529
- <article class="media content-section">
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- <div class="media-body" id="information">
531
-
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- <h2>{{ 'About this website' }}</h2>
533
- <br>
534
- <p> XspecT and ClAssT are provided by the
535
- <a href="https://www.bio.uni-frankfurt.de/43045195/Abt__Ebersberger___Biowissenschaften">
536
- Department for Applied Bioinformatics in Frankfurt (Germany). </a>
537
- </p>
538
- <p>XspecT is a bachelor thesis project of Dominik Sens. <br>
539
- ClAssT is a bachelor thesis project of Sam U. Gimbel.
540
- </p>
541
- <p> Charts are made with <a href="https://www.chartjs.org/">Chart.js</a>.</p>
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- </div>
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- </article>
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- {% endblock content %}
xspect/templates/home.html DELETED
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- {% extends "layouthome.html" %}
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- {% block content %}
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-
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- <article class="media content-section">
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-
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- <h1 style="text-align:center"> Welcome to XspecT and ClAssT!</h1>
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- <br>
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- <p style="margin-left: 320px; margin-right: 310px;text-align:center;">
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- XspecT is a tool to taxonomically assign bacterial Input-Data using Bloom Filters.
11
- XspecT performs a taxonomic assignment on the Species-Level while ClAssT, which is integrated into XspecT, uses Strain-Typing to
12
- identify International-Clones of A.baumannii. XspecT is also capable of screning for existance of Oxa-families.<br>
13
- For more information about the tool please visit our <a href="/about">information-page</a>.
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- </p>
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- <br>
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- <br>
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- <br>
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- <br>
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- <div class="row" style="text-align:center">
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- <div class="col-md-6 mx-auto">
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- <a href="/species" class="btn btn-primary" style="text-align:center;">
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- <h4 style="color:white">XspecT</h4>
23
- <p>Species-Level Assignment</p>
24
- <p>Strain Typing </p>
25
- <p>Oxa Screening</p>
26
- </a>
27
- </div>
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- </div>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- <br>
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- </div>
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- </article>
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-
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-
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- {% endblock content %}