XspecT 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl
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- xspect/classify.py +51 -38
- xspect/definitions.py +50 -10
- xspect/download_models.py +10 -2
- xspect/file_io.py +115 -48
- xspect/filter_sequences.py +36 -66
- xspect/main.py +44 -11
- xspect/mlst_feature/mlst_helper.py +3 -0
- xspect/mlst_feature/pub_mlst_handler.py +43 -1
- xspect/model_management.py +84 -14
- xspect/models/probabilistic_filter_mlst_model.py +75 -37
- xspect/models/probabilistic_filter_model.py +194 -12
- xspect/models/probabilistic_filter_svm_model.py +99 -6
- xspect/models/probabilistic_single_filter_model.py +66 -5
- xspect/models/result.py +77 -10
- xspect/ncbi.py +48 -12
- xspect/train.py +2 -1
- xspect/web.py +71 -13
- xspect/xspect-web/dist/assets/index-Ceo58xui.css +1 -0
- xspect/xspect-web/dist/assets/{index-CMG4V7fZ.js → index-Dt_UlbgE.js} +82 -77
- xspect/xspect-web/dist/index.html +2 -2
- xspect/xspect-web/src/App.tsx +4 -2
- xspect/xspect-web/src/api.tsx +23 -1
- xspect/xspect-web/src/components/filter-form.tsx +16 -3
- xspect/xspect-web/src/components/filtering-result.tsx +65 -0
- xspect/xspect-web/src/components/result.tsx +2 -2
- xspect/xspect-web/src/types.tsx +5 -0
- {xspect-0.5.1.dist-info → xspect-0.5.3.dist-info}/METADATA +1 -1
- {xspect-0.5.1.dist-info → xspect-0.5.3.dist-info}/RECORD +32 -31
- {xspect-0.5.1.dist-info → xspect-0.5.3.dist-info}/WHEEL +1 -1
- xspect/xspect-web/dist/assets/index-jIKg1HIy.css +0 -1
- {xspect-0.5.1.dist-info → xspect-0.5.3.dist-info}/entry_points.txt +0 -0
- {xspect-0.5.1.dist-info → xspect-0.5.3.dist-info}/licenses/LICENSE +0 -0
- {xspect-0.5.1.dist-info → xspect-0.5.3.dist-info}/top_level.txt +0 -0
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@@ -5,8 +5,8 @@
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<link rel="icon" type="image/svg+xml" href="/xspect-web/vite.svg" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>XspecT Web</title>
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<script type="module" crossorigin src="/xspect-web/assets/index-
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<link rel="stylesheet" crossorigin href="/xspect-web/assets/index-
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<script type="module" crossorigin src="/xspect-web/assets/index-Dt_UlbgE.js"></script>
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<link rel="stylesheet" crossorigin href="/xspect-web/assets/index-Ceo58xui.css">
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</head>
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<body>
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<div id="root"></div>
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xspect/xspect-web/src/App.tsx
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@@ -3,7 +3,8 @@ import Landing from "@/components/landing";
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import Classify from "@/components/classify"
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import Filter from "@/components/filter"
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import Models from "@/components/models"
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import
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import ResultPage from "@/components/result"
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import FilteringResultPage from "@/components/filtering-result"
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import { BrowserRouter as Router, Routes, Route } from "react-router-dom"
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import ModelDetails from "./components/models-details";
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@@ -18,7 +19,8 @@ function App() {
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<Route path="/filter" element={<Filter />} />
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<Route path="/models" element={<Models />} />
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<Route path="/models/:model_slug" element={<ModelDetails />} />
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<Route path="/result/:classification_uuid" element={<
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<Route path="/result/:classification_uuid" element={<ResultPage />} />
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<Route path="/filter-result/:filter_uuid" element={<FilteringResultPage />} />
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<Route path="*" element={<Landing />} />
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</Routes>
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</div>
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xspect/xspect-web/src/api.tsx
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@@ -1,5 +1,5 @@
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import axios from 'axios';
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import { Models, ClassificationResult, ModelMetadata } from '@/types';
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import { Models, ClassificationResult, FilteringResult, ModelMetadata } from '@/types';
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export async function getModels(): Promise<Models> {
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try {
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@@ -59,4 +59,26 @@ export async function getModelMetadata(modelSlug: string): Promise<ModelMetadata
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console.error('Error fetching model metadata:', error);
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throw new Error('Failed to fetch model metadata');
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}
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}
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export async function filterSequences(filter_type: string, genus : string, input_file : string, threshold : number, filter_species : string = "", sparse_sampling_step : number = 1): Promise<any> {
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try {
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const response = await axios.post(`/api/filter?filter_type=${filter_type}&genus=${genus}&input_file=${input_file}&threshold=${threshold}&filter_species=${filter_species}&step=${sparse_sampling_step}`);
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return response.data;
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} catch (error) {
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console.error('Error filtering sequences:', error);
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throw new Error('Failed to filter sequences');
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}
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}
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export async function getFilteringResult(filter_uuid: string): Promise<FilteringResult> {
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try {
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const response = await axios.get(`/api/filtering-result`, {
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params: { uuid: filter_uuid },
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});
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return response.data as FilteringResult;
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} catch (error) {
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console.error('Error fetching filtering result:', error);
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throw new Error('Failed to fetch filtering result');
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}
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}
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SelectTrigger,
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SelectValue,
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} from "@/components/ui/select"
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import { getModelMetadata, getModels, uploadFile } from "../api"
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import { filterSequences, getModelMetadata, getModels, uploadFile } from "../api"
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import {
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FileUpload,
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FileUploadDropzone,
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}, []);
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function onSubmit(data: z.infer<typeof FormSchema>) {
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const threshold = data.filter_mode === "threshold" ? data.threshold : -1;
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filterSequences(
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data.filter_type,
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data.model,
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data.input_file,
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threshold,
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data.filter_species,
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data.sparse_sampling_step
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).then((response) => {
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console.log("Filtering response:", response)
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navigate(`/filter-result/${response.uuid}`)
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})
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.catch((error) => {
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console.error("Error during filtering:", error)
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});
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}
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return (
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import { Link, useParams } from "react-router-dom"
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import { FilteringResult } from "../types";
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import { useState, useEffect, use } from "react";
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import { LoadingSpinner } from "./spinner";
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import { Separator } from "@/components/ui/separator";
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import { Button } from "./ui/button";
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import { getFilteringResult } from "../api";
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import { TriangleAlert } from "lucide-react";
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export default function FilteringResultPage() {
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const { filter_uuid } = useParams();
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const [filteringResult, setFilteringResult] = useState<FilteringResult | null>(null);
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useEffect(() => {
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const fetchResult = () => {
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if (filter_uuid) {
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getFilteringResult(filter_uuid).then((data) => {
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setFilteringResult(data);
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}).catch((error) => {
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console.error('Error fetching filtering result:', error);
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setTimeout(fetchResult, 500);
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});
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}
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};
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fetchResult();
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}, [filter_uuid, setFilteringResult]);
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return (
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<main className="flex-1 flex flex-col items-center justify-center p-4">
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<div className="w-1/2">
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{!filteringResult && (
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<div className="flex items-center justify-center">
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<LoadingSpinner className="size-10" />
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<span className="m-2 text-xl">Filtering...</span>
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</div>
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)}
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{filteringResult && (
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<>
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<h1 className="text-xl font-bold">Filtering Results</h1>
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<p>Your file was filtered successfully.</p>
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{filteringResult.message != "Filtering completed successfully." && (
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<div className="flex items-center gap-2 text-red-500">
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<TriangleAlert className="w-5 h-5" />
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<p>All sequences were filtered out.</p>
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</div>
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)}
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<Separator className="my-4 h-px" />
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<div className="flex flex-col gap-3 mt-4">
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{filteringResult.message == "Filtering completed successfully." && (
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<Button asChild>
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<a href={`${window.location.origin}/api/download-filtered?uuid=${filter_uuid}`} download>Download the filtered file</a>
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</Button>
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)}
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<Button variant="outline" asChild>
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<Link to={`/result/${filter_uuid}`}>View underlying classification results</Link>
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</Button>
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</div>
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</>
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)}
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</div>
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</main>
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)
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}
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export default function
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export default function ResultPage() {
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const { checkboxItems: contig_checkbox_items, setItems: setCheckboxItems } = useCheckboxItems();
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const { classification_uuid } = useParams();
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const [classificationResult, setClassificationResult] = useState<ClassificationResult | null>(null);
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{chartData && (<>
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<h1 className="text-xl font-bold">Classification Results</h1>
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<p>{classificationResult?.input_source} was classified using the <Link className="font-medium underline underline-offset-4" to={`/models/${modelMetadata?.model_slug}`}>{modelMetadata?.model_display_name} {modelMetadata?.model_type.toLowerCase()}</Link> model. {classificationResult?.sparse_sampling_step === 1 ? 'No sparse sampling was used.' : 'Sparse sampling was used with step ' + classificationResult?.sparse_sampling_step}</p>
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<p>{classificationResult?.input_source} was classified using the <Link className="font-medium underline underline-offset-4" to={`/models/${modelMetadata?.model_slug}`}>{modelMetadata?.model_display_name} {modelMetadata?.model_type.toLowerCase()}</Link> model. {classificationResult?.sparse_sampling_step === 1 ? 'No sparse sampling was used.' : 'Sparse sampling was used with step ' + classificationResult?.sparse_sampling_step + '.'}</p>
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<p className="mt-4"><b>Prediction:</b> {modelMetadata?.display_names[classificationResult?.prediction] || 'No prediction available.'}</p>
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<Button className="w-full mt-4" onClick={() => {
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const blob = new Blob([JSON.stringify(classificationResult, null, 2)], { type: 'application/json' });
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xspect/xspect-web/src/types.tsx
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num_kmers: { [subsequence: string]: number };
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prediction: string;
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}
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export interface FilteringResult {
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message: string;
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uuid : string;
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}
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xspect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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xspect/classify.py,sha256=
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xspect/classify.py,sha256=4E95JCMdLIaWQOlTVzWeNi3J4kAYsek__wMK8iiV_mI,3122
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xspect/definitions.py,sha256=FpdY1lzWG8mOLUIvL6YVCJX_jV_qdRSItk2yoodCQMg,2730
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xspect/download_models.py,sha256=VALcnowzkUpR-OAvgB5BUdEq9WnyNbli0CxH3OT40Rc,1121
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xspect/file_io.py,sha256=Y9BX5O2Ni-EEhWxq2Nh0zn0mzWfai-6s5f6ASE83eUA,8116
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xspect/filter_sequences.py,sha256=LOmhvK7SmUVpx5zsrCSySDFB1n6wbemBKysK34b4N-s,4574
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xspect/model_management.py,sha256=KhWL_TtbqZNIM8sakm_QPZAJMFgAFUwConqYKM7ekMk,5290
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xspect/ncbi.py,sha256=VRbFvtfGR4WTsc3buZE9UCabE3OJUTRphDRY20g63-E,11704
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xspect/train.py,sha256=jxjK4OqzTywmd5KGPou9A-doH8Nwhlv_xF4X7M6X_jI,11588
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[cmdk-group-heading]{font-size:var(--text-xs);line-height:var(--tw-leading,var(--text-xs--line-height))}.\[\&_\[cmdk-group-heading\]\]\:font-medium [cmdk-group-heading]{--tw-font-weight:var(--font-weight-medium);font-weight:var(--font-weight-medium)}.\[\&_\[cmdk-group-heading\]\]\:text-muted-foreground [cmdk-group-heading]{color:var(--muted-foreground)}.\[\&_\[cmdk-group\]\]\:px-2 [cmdk-group]{padding-inline:calc(var(--spacing)*2)}.\[\&_\[cmdk-group\]\:not\(\[hidden\]\)_\~\[cmdk-group\]\]\:pt-0 [cmdk-group]:not([hidden])~[cmdk-group]{padding-top:calc(var(--spacing)*0)}.\[\&_\[cmdk-input-wrapper\]_svg\]\:h-5 [cmdk-input-wrapper] svg{height:calc(var(--spacing)*5)}.\[\&_\[cmdk-input-wrapper\]_svg\]\:w-5 [cmdk-input-wrapper] svg{width:calc(var(--spacing)*5)}.\[\&_\[cmdk-input\]\]\:h-12 [cmdk-input]{height:calc(var(--spacing)*12)}.\[\&_\[cmdk-item\]\]\:px-2 [cmdk-item]{padding-inline:calc(var(--spacing)*2)}.\[\&_\[cmdk-item\]\]\:py-3 [cmdk-item]{padding-block:calc(var(--spacing)*3)}.\[\&_\[cmdk-item\]_svg\]\:h-5 [cmdk-item] svg{height:calc(var(--spacing)*5)}.\[\&_\[cmdk-item\]_svg\]\:w-5 [cmdk-item] svg{width:calc(var(--spacing)*5)}.\[\&_svg\]\:pointer-events-none svg{pointer-events:none}.\[\&_svg\]\:shrink-0 svg{flex-shrink:0}.\[\&_svg\:not\(\[class\*\=\'size-\'\]\)\]\:size-4 svg:not([class*=size-]){width:calc(var(--spacing)*4);height:calc(var(--spacing)*4)}.\[\&_svg\:not\(\[class\*\=\'text-\'\]\)\]\:text-muted-foreground svg:not([class*=text-]){color:var(--muted-foreground)}.\[\&_tr\]\:border-b tr{border-bottom-style:var(--tw-border-style);border-bottom-width:1px}.\[\&_tr\:last-child\]\:border-0 tr:last-child{border-style:var(--tw-border-style);border-width:0}.\[\&\:has\(\[role\=checkbox\]\)\]\:pr-0:has([role=checkbox]){padding-right:calc(var(--spacing)*0)}.\[\.border-b\]\:pb-6.border-b{padding-bottom:calc(var(--spacing)*6)}.\[\.border-t\]\:pt-6.border-t{padding-top:calc(var(--spacing)*6)}:is(.\*\:\[span\]\:last\:flex>*):is(span):last-child{display:flex}:is(.\*\:\[span\]\:last\:items-center>*):is(span):last-child{align-items:center}:is(.\*\:\[span\]\:last\:gap-2>*):is(span):last-child{gap:calc(var(--spacing)*2)}:is(.data-\[variant\=destructive\]\:\*\:\[svg\]\:\!text-destructive[data-variant=destructive]>*):is(svg){color:var(--destructive)!important}.\[\&\>\[role\=checkbox\]\]\:translate-y-\[2px\]>[role=checkbox]{--tw-translate-y:2px;translate:var(--tw-translate-x)var(--tw-translate-y)}.\[\&\>svg\]\:size-10>svg{width:calc(var(--spacing)*10);height:calc(var(--spacing)*10)}.\[\&\>svg\]\:h-2\.5>svg{height:calc(var(--spacing)*2.5)}.\[\&\>svg\]\:h-3>svg{height:calc(var(--spacing)*3)}.\[\&\>svg\]\:w-2\.5>svg{width:calc(var(--spacing)*2.5)}.\[\&\>svg\]\:w-3>svg{width:calc(var(--spacing)*3)}.\[\&\>svg\]\:text-muted-foreground>svg{color:var(--muted-foreground)}.\[\&\>tr\]\:last\:border-b-0>tr:last-child{border-bottom-style:var(--tw-border-style);border-bottom-width:0}.\[\&\[data-state\=open\]\>svg\]\:rotate-180[data-state=open]>svg{rotate:180deg}}:root{--radius:.3rem;--background:oklch(1 0 0);--foreground:oklch(.141 .005 285.823);--card:oklch(1 0 0);--card-foreground:oklch(.141 .005 285.823);--popover:oklch(1 0 0);--popover-foreground:oklch(.141 .005 285.823);--primary:oklch(.623 .214 259.815);--primary-foreground:oklch(.97 .014 254.604);--secondary:oklch(.967 .001 286.375);--secondary-foreground:oklch(.21 .006 285.885);--muted:oklch(.967 .001 286.375);--muted-foreground:oklch(.552 .016 285.938);--accent:oklch(.967 .001 286.375);--accent-foreground:oklch(.21 .006 285.885);--destructive:oklch(.577 .245 27.325);--border:oklch(.92 .004 286.32);--input:oklch(.92 .004 286.32);--ring:oklch(.623 .214 259.815);--chart-1:oklch(.646 .222 41.116);--chart-2:oklch(.6 .118 184.704);--chart-3:oklch(.398 .07 227.392);--chart-4:oklch(.828 .189 84.429);--chart-5:oklch(.769 .188 70.08);--sidebar:oklch(.985 0 0);--sidebar-foreground:oklch(.141 .005 285.823);--sidebar-primary:oklch(.623 .214 259.815);--sidebar-primary-foreground:oklch(.97 .014 254.604);--sidebar-accent:oklch(.967 .001 286.375);--sidebar-accent-foreground:oklch(.21 .006 285.885);--sidebar-border:oklch(.92 .004 286.32);--sidebar-ring:oklch(.623 .214 259.815)}.dark{--background:oklch(.141 .005 285.823);--foreground:oklch(.985 0 0);--card:oklch(.21 .006 285.885);--card-foreground:oklch(.985 0 0);--popover:oklch(.21 .006 285.885);--popover-foreground:oklch(.985 0 0);--primary:oklch(.546 .245 262.881);--primary-foreground:oklch(.379 .146 265.522);--secondary:oklch(.274 .006 286.033);--secondary-foreground:oklch(.985 0 0);--muted:oklch(.274 .006 286.033);--muted-foreground:oklch(.705 .015 286.067);--accent:oklch(.274 .006 286.033);--accent-foreground:oklch(.985 0 0);--destructive:oklch(.704 .191 22.216);--border:oklch(1 0 0/10%);--input:oklch(1 0 0/15%);--ring:oklch(.488 .243 264.376);--chart-1:oklch(.488 .243 264.376);--chart-2:oklch(.696 .17 162.48);--chart-3:oklch(.769 .188 70.08);--chart-4:oklch(.627 .265 303.9);--chart-5:oklch(.645 .246 16.439);--sidebar:oklch(.21 .006 285.885);--sidebar-foreground:oklch(.985 0 0);--sidebar-primary:oklch(.546 .245 262.881);--sidebar-primary-foreground:oklch(.379 .146 265.522);--sidebar-accent:oklch(.274 .006 286.033);--sidebar-accent-foreground:oklch(.985 0 0);--sidebar-border:oklch(1 0 0/10%);--sidebar-ring:oklch(.488 .243 264.376)}@property --tw-translate-x{syntax:"*";inherits:false;initial-value:0}@property --tw-translate-y{syntax:"*";inherits:false;initial-value:0}@property --tw-translate-z{syntax:"*";inherits:false;initial-value:0}@property --tw-rotate-x{syntax:"*";inherits:false}@property --tw-rotate-y{syntax:"*";inherits:false}@property --tw-rotate-z{syntax:"*";inherits:false}@property --tw-skew-x{syntax:"*";inherits:false}@property --tw-skew-y{syntax:"*";inherits:false}@property --tw-space-y-reverse{syntax:"*";inherits:false;initial-value:0}@property --tw-space-x-reverse{syntax:"*";inherits:false;initial-value:0}@property --tw-border-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-leading{syntax:"*";inherits:false}@property --tw-font-weight{syntax:"*";inherits:false}@property --tw-tracking{syntax:"*";inherits:false}@property --tw-ordinal{syntax:"*";inherits:false}@property --tw-slashed-zero{syntax:"*";inherits:false}@property --tw-numeric-figure{syntax:"*";inherits:false}@property --tw-numeric-spacing{syntax:"*";inherits:false}@property --tw-numeric-fraction{syntax:"*";inherits:false}@property --tw-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-shadow-color{syntax:"*";inherits:false}@property --tw-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-inset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-shadow-color{syntax:"*";inherits:false}@property --tw-inset-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-ring-color{syntax:"*";inherits:false}@property --tw-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-ring-color{syntax:"*";inherits:false}@property --tw-inset-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-ring-inset{syntax:"*";inherits:false}@property --tw-ring-offset-width{syntax:"<length>";inherits:false;initial-value:0}@property --tw-ring-offset-color{syntax:"*";inherits:false;initial-value:#fff}@property --tw-ring-offset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-outline-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-blur{syntax:"*";inherits:false}@property --tw-brightness{syntax:"*";inherits:false}@property --tw-contrast{syntax:"*";inherits:false}@property --tw-grayscale{syntax:"*";inherits:false}@property --tw-hue-rotate{syntax:"*";inherits:false}@property --tw-invert{syntax:"*";inherits:false}@property --tw-opacity{syntax:"*";inherits:false}@property --tw-saturate{syntax:"*";inherits:false}@property --tw-sepia{syntax:"*";inherits:false}@property --tw-drop-shadow{syntax:"*";inherits:false}@property --tw-drop-shadow-color{syntax:"*";inherits:false}@property --tw-drop-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-drop-shadow-size{syntax:"*";inherits:false}@property --tw-duration{syntax:"*";inherits:false}@property --tw-ease{syntax:"*";inherits:false}@keyframes spin{to{transform:rotate(360deg)}}@keyframes enter{0%{opacity:var(--tw-enter-opacity,1);transform:translate3d(var(--tw-enter-translate-x,0),var(--tw-enter-translate-y,0),0)scale3d(var(--tw-enter-scale,1),var(--tw-enter-scale,1),var(--tw-enter-scale,1))rotate(var(--tw-enter-rotate,0))}}@keyframes exit{to{opacity:var(--tw-exit-opacity,1);transform:translate3d(var(--tw-exit-translate-x,0),var(--tw-exit-translate-y,0),0)scale3d(var(--tw-exit-scale,1),var(--tw-exit-scale,1),var(--tw-exit-scale,1))rotate(var(--tw-exit-rotate,0))}}@keyframes accordion-down{0%{height:0}to{height:var(--radix-accordion-content-height,var(--bits-accordion-content-height,auto))}}@keyframes accordion-up{0%{height:var(--radix-accordion-content-height,var(--bits-accordion-content-height,auto))}to{height:0}}
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