XspecT 0.5.3__py3-none-any.whl → 0.6.0__py3-none-any.whl

xspect/web.py

@@ -1,17 +1,26 @@
 """FastAPI-based web application for XspecT."""
 
+# pylint: disable=too-many-arguments,too-many-positional-arguments
+
+
 from uuid import uuid4
 import json
 from shutil import copyfileobj
 import importlib.resources as pkg_resources
-from fastapi import APIRouter, FastAPI, HTTPException, UploadFile, BackgroundTasks
+from fastapi import (
+    APIRouter,
+    BackgroundTasks,
+    FastAPI,
+    HTTPException,
+    UploadFile,
+)
 from fastapi.responses import FileResponse, RedirectResponse
+from fastapi.staticfiles import StaticFiles
 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
 from xspect.train import train_from_ncbi
 from xspect import classify, filter_sequences
-from fastapi.staticfiles import StaticFiles
 
 app = FastAPI()
 app.mount(
@@ -72,7 +81,7 @@ def classify_post(
         )
         return {"message": "Classification started.", "uuid": uuid}
 
-    elif classification_type == "Species":
+    if classification_type == "Species":
         background_tasks.add_task(
             classify.classify_species,
             model,
@@ -119,7 +128,7 @@ def filter_post(
         )
         return {"message": "Genus filtering started.", "uuid": uuid}
 
-    elif filter_type == "Species":
+    if filter_type == "Species":
         if not filter_species:
             raise ValueError("filter_species must be provided for species filtering.")
         background_tasks.add_task(

{xspect-0.5.3.dist-info → xspect-0.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: XspecT
-Version: 0.5.3
+Version: 0.6.0
 Summary: Tool to monitor and characterize pathogens using Bloom filters.
 License: MIT License
         
@@ -45,6 +45,9 @@ Requires-Dist: xxhash
 Requires-Dist: fastapi
 Requires-Dist: uvicorn
 Requires-Dist: python-multipart
+Requires-Dist: mappy
+Requires-Dist: pysam
+Requires-Dist: numpy
 Provides-Extra: docs
 Requires-Dist: mkdocs-material; extra == "docs"
 Requires-Dist: mkdocs-include-markdown-plugin; extra == "docs"

{xspect-0.5.3.dist-info → xspect-0.6.0.dist-info}/RECORD

@@ -1,23 +1,27 @@
 xspect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/classify.py,sha256=4E95JCMdLIaWQOlTVzWeNi3J4kAYsek__wMK8iiV_mI,3122
-xspect/definitions.py,sha256=FpdY1lzWG8mOLUIvL6YVCJX_jV_qdRSItk2yoodCQMg,2730
+xspect/classify.py,sha256=fpXk8KobN9QQGSWu5pPR9g65bGxlOmcYEwZ5FJ5KSdM,4106
+xspect/definitions.py,sha256=eP2ttvoW9izCfMYqjLL6Y2oead44l74oHFKRDssTIF8,3506
 xspect/download_models.py,sha256=VALcnowzkUpR-OAvgB5BUdEq9WnyNbli0CxH3OT40Rc,1121
-xspect/file_io.py,sha256=Y9BX5O2Ni-EEhWxq2Nh0zn0mzWfai-6s5f6ASE83eUA,8116
-xspect/filter_sequences.py,sha256=LOmhvK7SmUVpx5zsrCSySDFB1n6wbemBKysK34b4N-s,4574
-xspect/main.py,sha256=Dt4ji-NgAUoR5DCcVXFxT0ZJSKgw7DJG8of3U9R6THw,13088
-xspect/model_management.py,sha256=KhWL_TtbqZNIM8sakm_QPZAJMFgAFUwConqYKM7ekMk,5290
-xspect/ncbi.py,sha256=VRbFvtfGR4WTsc3buZE9UCabE3OJUTRphDRY20g63-E,11704
-xspect/train.py,sha256=jxjK4OqzTywmd5KGPou9A-doH8Nwhlv_xF4X7M6X_jI,11588
-xspect/web.py,sha256=XD5G232DvGxVzX56-cWgAkss7m2dxk8t7-7WSuNXCIA,6949
+xspect/file_io.py,sha256=QX2nBtlLAexBdfUr7rtHLlWOuXiaKvfRdpn1Dn0avnY,8120
+xspect/filter_sequences.py,sha256=QKjgUCk3RBY3U9hHmyvSQeQt8n1voBna-NjOoTqdp3A,5196
+xspect/main.py,sha256=dhJa6mUneSI0nkwCWHqHrk9sZJgP0MkaPTSceSq1s4c,15463
+xspect/model_management.py,sha256=yWbCk6tUn7-OYpzH0BViX2oWr4cdNkEBjrvnaw5GPdQ,4893
+xspect/ncbi.py,sha256=RIwSJcPDREvk_YTNPfT34hQ4mb9nRKoXeNAS8wnLrHY,14413
+xspect/train.py,sha256=VQ5pISDtp0rlGwrYqK_4_OH9CE6n7L1DNZ3txeTty6M,12574
+xspect/web.py,sha256=kM4BZ3fA0f731EEXScAaiGrJZvjjfep1iC1iZemfazw,7039
+xspect/misclassification_detection/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xspect/misclassification_detection/mapping.py,sha256=xSibBi7-NoR74jakoYBmTW4Gy5FMfRDVF8H3ef5pElI,6698
+xspect/misclassification_detection/point_pattern_analysis.py,sha256=5ivksPAh0zGMVI33ETPrZ01tPE86ELOwI7-XpJNYsQA,3820
+xspect/misclassification_detection/simulate_reads.py,sha256=fxfKNSAwDT7Vnuh-_vgrMTLrfKihocZPU0gokNicey0,2009
 xspect/mlst_feature/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/mlst_feature/mlst_helper.py,sha256=MsBzMtqz2KW_YnLYOqfYdFTPkx2gC2T8chY9E_2JgLU,8236
-xspect/mlst_feature/pub_mlst_handler.py,sha256=t84obSvp0FUccUEsmNBjVxBj42kbzblJo41AYTvHfUk,7686
+xspect/mlst_feature/mlst_helper.py,sha256=pxRX_nRbrTSIFPf_FDV3dxR_FonmGtxttFgqNS7sIxE,8130
+xspect/mlst_feature/pub_mlst_handler.py,sha256=gX0bgAqXTaW9weWgxcbsiD7UtMGuDD9veE9mj42Ffm8,7685
 xspect/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/models/probabilistic_filter_mlst_model.py,sha256=s6JnqEHvh38Wg8qLD3-J_aU51REDolCY5DNAQtGAjGc,17630
-xspect/models/probabilistic_filter_model.py,sha256=3fAdQlOLvMZba9T-ej_qeGuhO_Fri8vAY_aG2vlvPFw,18350
-xspect/models/probabilistic_filter_svm_model.py,sha256=kzHYdkGFRD-ICviFc8EyawBi8P_9dzjiq0dOJc2rXys,10708
-xspect/models/probabilistic_single_filter_model.py,sha256=CoJeVe3Xw-DDbiBaFPGCpO3CPgiwG7i1Remz01uipSA,6880
-xspect/models/result.py,sha256=gKuyTUPEeXCPoVhj3T6J9LrWXG2usy91nzqeVNKcNTk,7028
+xspect/models/probabilistic_filter_mlst_model.py,sha256=w9ibUkAYA-DSOEkU8fBenlENrs8JwRRLaF5KO1HVKoM,17716
+xspect/models/probabilistic_filter_model.py,sha256=9CyNG-wcvjz1AORzr2hCO_laerYfen1OmWKbRh02nc8,23777
+xspect/models/probabilistic_filter_svm_model.py,sha256=WRXrAWr6f35B4VxgIhhLi1uj8RUZQAAhivjQdePsWhs,11094
+xspect/models/probabilistic_single_filter_model.py,sha256=vJvKZrAybYHq_UdKQ2GvvVwgTYwqRrL-nDDQZxb6RRc,6828
+xspect/models/result.py,sha256=v1wslD4RHgoTSwqOVtejfSbEhg4jZ0CDPG55nyhklUg,7185
 xspect/xspect-web/.gitignore,sha256=_nGOe6uxTzy60tl_CIibnOUhXtP-DkOyuM-_s7m4ROg,253
 xspect/xspect-web/README.md,sha256=Fa5cCk66ohbqD_AAVgnXUZLhuzshnLxhlUFhxyscScc,1942
 xspect/xspect-web/components.json,sha256=5emhfq5JRW9J8Zga-1N5jAcj4B-r8VREXnH7Z6tZGNk,425
@@ -78,9 +82,9 @@ xspect/xspect-web/src/components/ui/switch.tsx,sha256=uIqRXtd41ba0eusIEUWVyYZv82
 xspect/xspect-web/src/components/ui/table.tsx,sha256=M2-TIHKwPFWuXrwysSufdQRSMJT-K9jPzGOokfU6PXo,2463
 xspect/xspect-web/src/components/ui/tabs.tsx,sha256=BImHKcdDCtrS3CCV1AGgn8qg0b65RB5P-QdH49IAhx0,1955
 xspect/xspect-web/src/lib/utils.ts,sha256=66ibdQiEHKftZBq1OMLmOKqWma1BkO-O60rc1IQYwLE,165
-xspect-0.5.3.dist-info/licenses/LICENSE,sha256=bhBGDKIRUVwYIHGOGO5hshzuVHyqFJajvSOA3XXOLKI,1094
-xspect-0.5.3.dist-info/METADATA,sha256=T9yTZsMadZgZXFx3Uezd75GGg9iTnELTwcAeiX5G51k,4569
-xspect-0.5.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-xspect-0.5.3.dist-info/entry_points.txt,sha256=L7qliX3pIuwupQxpuOSsrBJCSHYPOPNEzH8KZKQGGUw,43
-xspect-0.5.3.dist-info/top_level.txt,sha256=hdoa4cnBv6OVzpyhMmyxpJxEydH5n2lDciy8urc1paE,7
-xspect-0.5.3.dist-info/RECORD,,
+xspect-0.6.0.dist-info/licenses/LICENSE,sha256=bhBGDKIRUVwYIHGOGO5hshzuVHyqFJajvSOA3XXOLKI,1094
+xspect-0.6.0.dist-info/METADATA,sha256=_3lkPNVzF3iUOFGFaGRavSPfuJ_wdCQODA0qfU5GXJg,4632
+xspect-0.6.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+xspect-0.6.0.dist-info/entry_points.txt,sha256=L7qliX3pIuwupQxpuOSsrBJCSHYPOPNEzH8KZKQGGUw,43
+xspect-0.6.0.dist-info/top_level.txt,sha256=hdoa4cnBv6OVzpyhMmyxpJxEydH5n2lDciy8urc1paE,7
+xspect-0.6.0.dist-info/RECORD,,