XspecT 0.5.1__py3-none-any.whl → 0.5.2__py3-none-any.whl

xspect/models/result.py

@@ -14,9 +14,22 @@ class ModelResult:
         hits: dict[str, dict[str, int]],
         num_kmers: dict[str, int],
         sparse_sampling_step: int = 1,
-        prediction: str = None,
-        input_source: str = None,
+        prediction: str | None = None,
+        input_source: str | None = None,
     ):
+        """
+        Initialize the ModelResult object.
+
+        Args:
+            model_slug (str): The slug of the model.
+            hits (dict[str, dict[str, int]]): A dictionary where keys are subsequence names
+                and values are dictionaries with labels as keys and hit counts as values.
+            num_kmers (dict[str, int]): A dictionary where keys are subsequence names
+                and values are the total number of k-mers for that subsequence.
+            sparse_sampling_step (int): The step size for sparse sampling, default is 1.
+            prediction (str | None): The prediction made by the model, default is None.
+            input_source (str | None): The source of the input data, default is None.
+        """
         if "total" in hits:
             raise ValueError(
                 "'total' is a reserved key and cannot be used as a subsequence"
@@ -29,7 +42,16 @@ class ModelResult:
         self.input_source = input_source
 
     def get_scores(self) -> dict:
-        """Return the scores of the model."""
+        """
+        Return the scores of the model.
+
+        The scores are calculated as the number of hits divided by the total number of k-mers
+        for each subsequence and label. The scores are rounded to two decimal places.
+
+        Returns:
+            dict: A dictionary where keys are subsequence names and values are dictionaries
+                with labels as keys and scores as values. Also includes a 'total' key for overall scores.
+        """
         scores = {
             subsequence: {
                 label: round(hits / self.num_kmers[subsequence], 2)
@@ -50,20 +72,37 @@ class ModelResult:
         return scores
 
     def get_total_hits(self) -> dict[str, int]:
-        """Return the total hits of the model."""
+        """
+        Return the total hits of the model.
+
+        The total hits are calculated by summing the hits for each label across all subsequences.
+
+        Returns:
+            dict: A dictionary where keys are labels and values are the total number of hits for that label.
+        """
         total_hits = {label: 0 for label in list(self.hits.values())[0]}
-        for _, subseuqence_hits in self.hits.items():
-            for label, hits in subseuqence_hits.items():
+        for _, subsequence_hits in self.hits.items():
+            for label, hits in subsequence_hits.items():
                 total_hits[label] += hits
         return total_hits
 
     def get_filter_mask(self, label: str, filter_threshold: float) -> dict[str, bool]:
-        """Return a mask for filtered subsequences.
+        """
+        Return a mask for filtered subsequences.
 
         The mask is a dictionary with subsequence names as keys and boolean values
         indicating whether the subsequence is above the filter threshold for the given label.
         A value of -1 for filter_threshold indicates that the subsequence with the maximum score
         for the given label should be returned.
+
+        Args:
+            label (str): The label for which to filter the subsequences.
+            filter_threshold (float): The threshold for filtering subsequences. Must be between 0 and 1,
+                or -1 to return the subsequence with the maximum score for the label.
+
+        Returns:
+            dict[str, bool]: A dictionary where keys are subsequence names and values are booleans
+                indicating whether the subsequence meets the filter criteria for the given label.
         """
         if filter_threshold < 0 and not filter_threshold == -1 or filter_threshold > 1:
             raise ValueError("The filter threshold must be between 0 and 1.")
@@ -84,7 +123,19 @@ class ModelResult:
     def get_filtered_subsequence_labels(
         self, label: str, filter_threshold: float = 0.7
     ) -> list[str]:
-        """Return the labels of filtered subsequences."""
+        """
+        Return the labels of filtered subsequences.
+
+        This method filters subsequences based on the scores for a given label and a filter threshold.
+
+        Args:
+            label (str): The label for which to filter the subsequences.
+            filter_threshold (float): The threshold for filtering subsequences. Must be between 0 and 1,
+                or -1 to return the subsequence with the maximum score for the label.
+
+        Returns:
+            list[str]: A list of subsequence names that meet the filter criteria for the given label.
+        """
         return [
             subsequence
             for subsequence, mask in self.get_filter_mask(
@@ -94,7 +145,15 @@ class ModelResult:
         ]
 
     def to_dict(self) -> dict:
-        """Return the result as a dictionary."""
+        """
+        Return the result as a dictionary.
+
+        This method converts the ModelResult object into a dictionary format suitable for serialization.
+
+        Returns:
+            dict: A dictionary representation of the ModelResult object, including model slug,
+            sparse sampling step, hits, scores, number of k-mers, input source, and prediction if available.
+        """
         res = {
             "model_slug": self.model_slug,
             "sparse_sampling_step": self.sparse_sampling_step,
@@ -110,6 +169,14 @@ class ModelResult:
         return res
 
     def save(self, path: Path) -> None:
-        """Save the result as a JSON file."""
+        """
+        Save the result as a JSON file.
+
+        This method serializes the ModelResult object to a JSON file at the specified path.
+
+        Args:
+            path (Path): The path where the JSON file will be saved.
+        """
+        path.parent.mkdir(exist_ok=True, parents=True)
         with open(path, "w", encoding="utf-8") as f:
             f.write(dumps(self.to_dict(), indent=4))

xspect/ncbi.py

@@ -27,26 +27,35 @@ class AssemblySource(Enum):
 
 
 class NCBIHandler:
-    """This class uses the NCBI Datasets API to get the taxonomy tree of a given Taxon.
+    """
+    This class uses the NCBI Datasets API to get data about taxa and their assemblies.
 
-    The taxonomy tree consists of only the next children to the parent taxon.
-    The children are only of the next lower rank of the parent taxon.
+    It provides methods to get taxon IDs, species, names, accessions, and download assemblies.
+    It also enforces rate limiting to comply with NCBI's API usage policies.
     """
 
     def __init__(
         self,
         api_key: str | None = None,
     ):
-        """Initialise the NCBI handler."""
+        """
+        Initialise the NCBI handler.
+
+        This method sets up the base URL for the NCBI Datasets API and initializes the rate limiting parameters.
+
+        Args:
+            api_key (str | None): The NCBI API key. If None, the handler will use the public API without an API key.
+        """
         self.api_key = api_key
         self.base_url = "https://api.ncbi.nlm.nih.gov/datasets/v2"
-        self.last_request_time = 0
+        self.last_request_time = 0.0
         self.min_interval = (
             1 / 10 if api_key else 1 / 5
         )  # NCBI allows 10 requests per second with if an API key, otherwise 5 requests per second
 
-    def _enforce_rate_limit(self):
-        """Enforce rate limiting for the NCBI Datasets API.
+    def _enforce_rate_limit(self) -> None:
+        """
+        Enforce rate limiting for the NCBI Datasets API.
 
         This method ensures that the requests to the API are limited to 5 requests per second
         without an API key and 10 requests per second with an API key.
@@ -59,7 +68,11 @@ class NCBIHandler:
         self.last_request_time = now
 
     def _make_request(self, endpoint: str, timeout: int = 15) -> dict:
-        """Make a request to the NCBI Datasets API.
+        """
+        Make a request to the NCBI Datasets API.
+
+        This method constructs the full URL for the API endpoint, adds the necessary headers (including the API key if provided),
+        and makes a GET request to the API. It also enforces rate limiting before making the request.
 
         Args:
             endpoint (str): The endpoint to make the request to.
@@ -239,7 +252,20 @@ class NCBIHandler:
     def get_highest_quality_accessions(
         self, taxon_id: int, assembly_source: AssemblySource, count: int
     ) -> list[str]:
-        """Get the highest quality accessions for a given taxon id (based on the assembly level)."""
+        """
+        Get the highest quality accessions for a given taxon id (based on the assembly level).
+
+        This function iterates through the assembly levels in order of quality and retrieves accessions
+        until the specified count is reached. It ensures that the accessions are unique and sorted by quality.
+
+        Args:
+            taxon_id (int): The taxon id to get the accessions for.
+            assembly_source (AssemblySource): The assembly source to get the accessions for.
+            count (int): The number of accessions to get.
+
+        Returns:
+            list[str]: A list containing the highest quality accessions.
+        """
         accessions = []
         for assembly_level in list(AssemblyLevel):
             accessions += self.get_accessions(
@@ -253,7 +279,16 @@ class NCBIHandler:
         return list(set(accessions))[:count]  # Remove duplicates and limit to count
 
     def download_assemblies(self, accessions: list[str], output_dir: Path) -> None:
-        """Download assemblies for a list of accessions."""
+        """
+        Download assemblies for a list of accessions.
+
+        This function makes a request to the NCBI Datasets API to download the assemblies for the given accessions.
+        It saves the downloaded assemblies as a zip file in the specified output directory.
+
+        Args:
+            accessions (list[str]): A list of accessions to download.
+            output_dir (Path): The directory where the downloaded assemblies will be saved.
+        """
         endpoint = f"/genome/accession/{','.join(accessions)}/download?include_annotation_type=GENOME_FASTA"
 
         self._enforce_rate_limit()

xspect/train.py

@@ -187,7 +187,8 @@ def train_from_ncbi(
     author_email: str | None = None,
     ncbi_api_key: str | None = None,
 ):
-    """Train a model using NCBI assembly data for a given genus.
+    """
+    Train a model using NCBI assembly data for a given genus.
 
     This function trains a probabilistic filter model using the assembly data from NCBI.
     The training data is downloaded and processed, and the model is saved to the

xspect/web.py

@@ -5,7 +5,7 @@ import json
 from shutil import copyfileobj
 import importlib.resources as pkg_resources
 from fastapi import APIRouter, FastAPI, HTTPException, UploadFile, BackgroundTasks
-from fastapi.responses import RedirectResponse
+from fastapi.responses import FileResponse, RedirectResponse
 from xspect.definitions import get_xspect_runs_path, get_xspect_upload_path
 from xspect.download_models import download_test_models
 import xspect.model_management as mm
@@ -85,36 +85,92 @@ def classify_post(
     )
 
 
-router.post("/filter")
-
-
+@router.post("/filter")
 def filter_post(
     filter_type: str,
-    model: str,
+    genus: str,
     input_file: str,
     threshold: float,
-    filter_species: str = None,
+    background_tasks: BackgroundTasks,
+    filter_species: str | None = None,
+    step: int = 1,
 ):
     """Filter sequences."""
     input_path = get_xspect_upload_path() / input_file
-    output_path = get_xspect_upload_path() / f"filtered_{input_file}"
+
+    uuid = str(uuid4())
+    filter_output_path = get_xspect_runs_path() / f"filtered_{uuid}.fasta"
+    classification_output_path = get_xspect_runs_path() / f"result_{uuid}.json"
 
     if not input_path.exists():
         raise FileNotFoundError(f"File {input_path} does not exist.")
 
     if filter_type == "Genus":
-        filter_sequences.filter_genus(model, input_path, output_path, threshold)
-        return {"message": "Genus Filtering started."}
+        background_tasks.add_task(
+            filter_sequences.filter_genus,
+            genus,
+            input_path,
+            filter_output_path,
+            threshold,
+            classification_output_path,
+            step,
+        )
+        return {"message": "Genus filtering started.", "uuid": uuid}
 
     elif filter_type == "Species":
-        filter_sequences.filter_species(
-            model, filter_species, input_path, output_path, threshold
+        if not filter_species:
+            raise ValueError("filter_species must be provided for species filtering.")
+        background_tasks.add_task(
+            filter_sequences.filter_species,
+            genus,
+            filter_species,
+            input_path,
+            filter_output_path,
+            threshold,
+            classification_output_path,
+            step,
         )
-        return {"message": "Species Filtering started."}
+        return {"message": "Species filtering started.", "uuid": uuid}
 
     raise NotImplementedError(f"Filter type {filter_type} is not implemented.")
 
 
+@router.get("/filtering-result")
+def get_filtering_result(uuid: str):
+    """Get filtering result."""
+    result_path = get_xspect_runs_path() / f"result_{uuid}.json"
+    filtered_path = get_xspect_runs_path() / f"filtered_{uuid}.fasta"
+    if not result_path.exists():
+        raise HTTPException(
+            status_code=404, detail="No result found for the specified uuid."
+        )
+    if not filtered_path.exists():
+        return {
+            "message": "Filtering completed, but no sequences met the criteria.",
+            "uuid": uuid,
+        }
+    return {
+        "message": "Filtering completed successfully.",
+        "uuid": uuid,
+    }
+
+
+@router.get("/download-filtered")
+def download_filtered(uuid: str):
+    """Download filtered sequences."""
+    filtered_path = get_xspect_runs_path() / f"filtered_{uuid}.fasta"
+    if not filtered_path.exists():
+        raise HTTPException(
+            status_code=404,
+            detail="No filtered sequences found for the specified uuid.",
+        )
+    return FileResponse(
+        filtered_path,
+        media_type="application/octet-stream",
+        filename=filtered_path.name,
+    )
+
+
 @router.post("/train")
 def train(genus: str, background_tasks: BackgroundTasks, svm_steps: int = 1):
     """Train NCBI model."""

xspect/xspect-web/dist/assets/index-Ceo58xui.css

@@ -0,0 +1 @@
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[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 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--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 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