XspecT 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl

{XspecT-0.2.3.dist-info → XspecT-0.2.5.dist-info}/METADATA

@@ -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.dist-info → XspecT-0.2.5.dist-info}/RECORD

@@ -3,14 +3,14 @@ xspect/definitions.py,sha256=gg6NvT8ypNzlnJvMMo3nHsyh8DHFFu41lOfnILkRDpE,1215
 xspect/download_filters.py,sha256=ByE7Oggx-AyJ02Wirk_wcJHNdRDrJMfjwhmUe5tgWbE,741
 xspect/fastapi.py,sha256=C8pBBiqM6UdedLZgzfL_YYRuy98aPj8dcw_CLFrtMMc,3260
 xspect/file_io.py,sha256=zKhl6Fd9KZAYiD8YgIyje5TbDYk5lxMp1WUrNkGSBo8,2779
-xspect/main.py,sha256=EjtgwipOLH8rnJ79pWRAjDVx8FUtinYJy7jd_eYr_wQ,3624
+xspect/main.py,sha256=eOA9PAeq3VvPWWoOZxXFErvPNW-ANzOxqMsbQJPCvDw,3651
 xspect/model_management.py,sha256=w0aqjLUoixCokyKTYrcN1vih5IoLYLJG9p8aeYdVc8Y,3560
 xspect/pipeline.py,sha256=h7duhVZ-hupwO_KQPstzFo8KMfMI2yleb9HmtTiMjic,7219
 xspect/run.py,sha256=OJ7pCFqva3AhIYklKjVnqWGooVRO7S3b56kIAy-xabY,1189
 xspect/train.py,sha256=khC1lldqfr4NvzLUiSJjSlh7DBG1ePielvQMiB29Hl8,10399
 xspect/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 xspect/models/probabilistic_filter_model.py,sha256=ImyNRzR7jf2CBPGI65ItG0_eYmrQjo9soQYlsM0r-P0,9829
-xspect/models/probabilistic_filter_svm_model.py,sha256=9Q4SBAzgbqATpS2E3IoardPpBwqkyrYSnrMwh0zwSag,5420
+xspect/models/probabilistic_filter_svm_model.py,sha256=Z_aAigE_fC_gm80hRfxvROHGs6LuBqZnATHPpAkQGQE,5466
 xspect/models/probabilistic_single_filter_model.py,sha256=nDAd_-_Ci2eH0KOJtf4wA-w63FMq9rGSR1LGiIA-gdw,3884
 xspect/models/result.py,sha256=vHUEFXvbFyB8WmasXp99IrztjwaxH1f9QMFiRUPe40Q,4824
 xspect/train_filter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -22,9 +22,9 @@ xspect/train_filter/ncbi_api/download_assemblies.py,sha256=MB_mxSjCTL05DqIt1WQem
 xspect/train_filter/ncbi_api/ncbi_assembly_metadata.py,sha256=puzDIws-yyBAEHwSAIYUM7g8FpLFmvOKh5xH1EsY8ZE,3830
 xspect/train_filter/ncbi_api/ncbi_children_tree.py,sha256=_8puOsnsKp5lsMV2gZY1ijkfD_BZKG9eXZCX09qph5E,1819
 xspect/train_filter/ncbi_api/ncbi_taxon_metadata.py,sha256=O6JDXC4E6AYaf7NPnb34eSJyZhMB8r--bjoVF_ZsEdA,1868
-XspecT-0.2.3.dist-info/LICENSE,sha256=bhBGDKIRUVwYIHGOGO5hshzuVHyqFJajvSOA3XXOLKI,1094
-XspecT-0.2.3.dist-info/METADATA,sha256=6z-4ftDDKIA48kGcXB3HJoELmdM4X0f9uYCk0p5jHGU,4826
-XspecT-0.2.3.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
-XspecT-0.2.3.dist-info/entry_points.txt,sha256=L7qliX3pIuwupQxpuOSsrBJCSHYPOPNEzH8KZKQGGUw,43
-XspecT-0.2.3.dist-info/top_level.txt,sha256=hdoa4cnBv6OVzpyhMmyxpJxEydH5n2lDciy8urc1paE,7
-XspecT-0.2.3.dist-info/RECORD,,
+XspecT-0.2.5.dist-info/LICENSE,sha256=bhBGDKIRUVwYIHGOGO5hshzuVHyqFJajvSOA3XXOLKI,1094
+XspecT-0.2.5.dist-info/METADATA,sha256=NDw2i1MawAjAkybDXzaQfIIGFI4sw86MSlQJ8z6vkWs,4834
+XspecT-0.2.5.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+XspecT-0.2.5.dist-info/entry_points.txt,sha256=L7qliX3pIuwupQxpuOSsrBJCSHYPOPNEzH8KZKQGGUw,43
+XspecT-0.2.5.dist-info/top_level.txt,sha256=hdoa4cnBv6OVzpyhMmyxpJxEydH5n2lDciy8urc1paE,7
+XspecT-0.2.5.dist-info/RECORD,,

{XspecT-0.2.3.dist-info → XspecT-0.2.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (73.0.1)
+Generator: setuptools (74.1.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

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/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]),
         )