.gitignore
LICENSE
README.md
pyproject.toml
.github/workflows/black.yml
.github/workflows/docs.yml
.github/workflows/test.yml
data/Results/Readme.txt
data/Results/Strain-Typing/Assemblys as reference, all k-mers.csv
data/Results/Strain-Typing/Assemblys as reference, quick run.csv
data/Results/Strain-Typing/Core-Genome as Reference, quick run.csv
data/Results/Strain-Typing/Core-Genome as reference, all k-mers.csv
data/Results/Strain-Typing/Reads as Input, Assembly as Reference, 15% of the nucleotides changed.csv
data/Results/Strain-Typing/Reads as Input, Assembly as Reference.csv
data/Results/Strain-Typing/Reads as Input, Core-Genome as Reference, 15% of the nucleotides changed.csv
data/Results/Strain-Typing/Reads as Input, Core-Genome as Reference.csv
data/Results/Strain-Typing/StratifiedKFold.py
data/Results/Strain-Typing/genomes_and_labels.csv
data/Results/XspecT_mini_csv/README
docs/Makefile
docs/conf.py
docs/index.md
docs/make.bat
docs/quickstart.md
docs/Instructions/pictures/About.png
docs/Instructions/pictures/AddFilter.png
docs/Instructions/pictures/AddSpecies1.png
docs/Instructions/pictures/AddSpecies2.png
docs/Instructions/pictures/BF.png
docs/Instructions/pictures/ClAssT_Ergebnis1.png
docs/Instructions/pictures/ClAssT_Ergebnis2.png
docs/Instructions/pictures/ClAssT_Ergebnis3.png
docs/Instructions/pictures/ClAssT_Hauptseite.png
docs/Instructions/pictures/CommandLine_Input.png
docs/Instructions/pictures/CommandLine_results.png
docs/Instructions/pictures/CommandLine_whole.png
docs/Instructions/pictures/How2Use.png
docs/Instructions/pictures/HowtouseAspecT.png
docs/Instructions/pictures/XspecT_Ergebnis1.png
docs/Instructions/pictures/XspecT_Ergebnis2.png
docs/Instructions/pictures/XspecT_Ergebnis3.png
docs/Instructions/pictures/XspecT_Ergebnis4.png
docs/Instructions/pictures/XspecT_Hauptseite.png
docs/Instructions/pictures/XspecT_Runtime.png
docs/Instructions/pictures/XspecT_Runtime_Oxa.png
docs/Instructions/pictures/XspecT_Startseite.png
docs/Instructions/pictures/change_pw.png
docs/Instructions/pictures/modify_vecs.png
docs/Instructions/pictures/secretkey.png
docs/img/logo.png
src/XspecT.egg-info/PKG-INFO
src/XspecT.egg-info/SOURCES.txt
src/XspecT.egg-info/dependency_links.txt
src/XspecT.egg-info/entry_points.txt
src/XspecT.egg-info/requires.txt
src/XspecT.egg-info/top_level.txt
src/xspect/BF_v2.py
src/xspect/Bootstrap.py
src/xspect/Classifier.py
src/xspect/OXA_Table.py
src/xspect/WebApp.py
src/xspect/XspecT_mini.py
src/xspect/XspecT_trainer.py
src/xspect/__init__.py
src/xspect/download_filters.py
src/xspect/file_io.py
src/xspect/main.py
src/xspect/map_kmers.py
src/xspect/search_filter.py
src/xspect/static/How-To.png
src/xspect/static/Logo.png
src/xspect/static/Logo2.png
src/xspect/static/Workflow_AspecT.png
src/xspect/static/Workflow_ClAssT.png
src/xspect/static/js.js
src/xspect/static/main.css
src/xspect/templates/400.html
src/xspect/templates/401.html
src/xspect/templates/404.html
src/xspect/templates/500.html
src/xspect/templates/about.html
src/xspect/templates/home.html
src/xspect/templates/layoutabout.html
src/xspect/templates/layouthome.html
src/xspect/templates/layoutspecies.html
src/xspect/templates/species.html
src/xspect/train_filter/README_XspecT_Erweiterung.md
src/xspect/train_filter/__init__.py
src/xspect/train_filter/create_svm.py
src/xspect/train_filter/extract_and_concatenate.py
src/xspect/train_filter/get_paths.py
src/xspect/train_filter/html_scrap.py
src/xspect/train_filter/interface_XspecT.py
src/xspect/train_filter/k_mer_count.py
src/xspect/train_filter/ncbi_api/__init__.py
src/xspect/train_filter/ncbi_api/download_assemblies.py
src/xspect/train_filter/ncbi_api/ncbi_assembly_metadata.py
src/xspect/train_filter/ncbi_api/ncbi_children_tree.py
src/xspect/train_filter/ncbi_api/ncbi_taxon_metadata.py
tests/__init__.py
tests/conftest.py
tests/test_cli.py
tests/test_file_io.py
tests/test_flask.py