XspecT 0.2.3__tar.gz → 0.2.5__tar.gz

{xspect-0.2.3/src/XspecT.egg-info → xspect-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: XspecT
-Version: 0.2.3
+Version: 0.2.5
 Summary: Tool to monitor and characterize pathogens using Bloom filters.
 License: MIT License
         
@@ -60,7 +60,8 @@ Requires-Dist: pytest-cov; extra == "test"
 [![linting: pylint](https://img.shields.io/badge/linting-pylint-yellowgreen)](https://github.com/pylint-dev/pylint)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-<img src="/src/docs/img/logo.png" height="50%" width="50%">
+<img src="/docs/img/logo.png" height="50%" width="50%">
+
 <!-- start intro -->
 XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or sub-type level using [Bloom Filters] and a [Support Vector Machine]. It also identifies existing [blaOxa-genes] and provides a list of relevant research papers for further information.
 <br/><br/>
@@ -84,7 +85,7 @@ To install Xspect, please download the lastest 64 bit Python version and install
 ```
 pip install xspect
 ```
-Please note that Apple Silicon is currently not supported.
+Please note that Windows and Alpine Linux is currently not supported.
 
 ## Usage
 ### Get the Bloomfilters

{xspect-0.2.3 → xspect-0.2.5}/README.md

@@ -3,7 +3,8 @@
 [![linting: pylint](https://img.shields.io/badge/linting-pylint-yellowgreen)](https://github.com/pylint-dev/pylint)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-<img src="/src/docs/img/logo.png" height="50%" width="50%">
+<img src="/docs/img/logo.png" height="50%" width="50%">
+
 <!-- start intro -->
 XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or sub-type level using [Bloom Filters] and a [Support Vector Machine]. It also identifies existing [blaOxa-genes] and provides a list of relevant research papers for further information.
 <br/><br/>
@@ -27,7 +28,7 @@ To install Xspect, please download the lastest 64 bit Python version and install
 ```
 pip install xspect
 ```
-Please note that Apple Silicon is currently not supported.
+Please note that Windows and Alpine Linux is currently not supported.
 
 ## Usage
 ### Get the Bloomfilters

{xspect-0.2.3 → xspect-0.2.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "XspecT"
-version = "0.2.3"
+version = "0.2.5"
 description = "Tool to monitor and characterize pathogens using Bloom filters."
 readme = {file = "README.md", content-type = "text/markdown"}
 license = {file = "LICENSE"}

{xspect-0.2.3 → xspect-0.2.5/src/XspecT.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: XspecT
-Version: 0.2.3
+Version: 0.2.5
 Summary: Tool to monitor and characterize pathogens using Bloom filters.
 License: MIT License
         
@@ -60,7 +60,8 @@ Requires-Dist: pytest-cov; extra == "test"
 [![linting: pylint](https://img.shields.io/badge/linting-pylint-yellowgreen)](https://github.com/pylint-dev/pylint)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-<img src="/src/docs/img/logo.png" height="50%" width="50%">
+<img src="/docs/img/logo.png" height="50%" width="50%">
+
 <!-- start intro -->
 XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or sub-type level using [Bloom Filters] and a [Support Vector Machine]. It also identifies existing [blaOxa-genes] and provides a list of relevant research papers for further information.
 <br/><br/>
@@ -84,7 +85,7 @@ To install Xspect, please download the lastest 64 bit Python version and install
 ```
 pip install xspect
 ```
-Please note that Apple Silicon is currently not supported.
+Please note that Windows and Alpine Linux is currently not supported.
 
 ## Usage
 ### Get the Bloomfilters

{xspect-0.2.3 → xspect-0.2.5}/src/xspect/main.py

@@ -2,6 +2,7 @@
 
 from pathlib import Path
 import datetime
+import uuid
 import click
 import uvicorn
 from xspect import fastapi
@@ -77,7 +78,7 @@ def classify(genus, path, meta, step):
     for idx, file_path in enumerate(file_paths):
         run = pipeline.run(file_path)
         time_str = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
-        save_path = get_xspect_runs_path() / f"run_{time_str}.json"
+        save_path = get_xspect_runs_path() / f"run_{time_str}_{uuid.uuid4()}.json"
         run.save(save_path)
         print(
             f"[{idx+1}/{len(file_paths)}] Run finished. Results saved to '{save_path}'."

{xspect-0.2.3 → xspect-0.2.5}/src/xspect/models/probabilistic_filter_svm_model.py

@@ -107,7 +107,7 @@ class ProbabilisticFilterSVMModel(ProbabilisticFilterModel):
         ),
         filter_ids: list[str] = None,
         step: int = 1,
-    ) -> dict:
+    ) -> ModelResult:
         """Predict the labels of the sequences"""
         # get scores and format them for the SVM
         res = super().predict(sequence_input, filter_ids, step=step)
@@ -119,6 +119,7 @@ class ProbabilisticFilterSVMModel(ProbabilisticFilterModel):
             self.slug(),
             res.hits,
             res.num_kmers,
+            sparse_sampling_step=step,
             prediction=str(svm.predict(svm_scores)[0]),
         )