.gitignore
LICENSE.txt
Makefile
README.md
flake.nix
pyproject.toml
.github/workflows/package_and_test.yml
.github/workflows/publish_to_pypi.yml
.streamlit/config.toml
EFMCalculator.egg-info/PKG-INFO
EFMCalculator.egg-info/SOURCES.txt
EFMCalculator.egg-info/dependency_links.txt
EFMCalculator.egg-info/entry_points.txt
EFMCalculator.egg-info/requires.txt
EFMCalculator.egg-info/top_level.txt
efmcalculator/StateMachine.py
efmcalculator/__init__.py
efmcalculator/_version.py
efmcalculator/cli.py
efmcalculator/constants.py
efmcalculator/utilities.py
efmcalculator/data/__init__.py
efmcalculator/data/gam_df.csv
efmcalculator/ingest/EFMSequence.py
efmcalculator/ingest/__init__.py
efmcalculator/ingest/bad_state_mitigation.py
efmcalculator/ingest/parse_inputs.py
efmcalculator/pipeline/__init__.py
efmcalculator/pipeline/classify_srs_rmd.py
efmcalculator/pipeline/classify_ssr.py
efmcalculator/pipeline/detection_strats.py
efmcalculator/pipeline/features.py
efmcalculator/pipeline/filtering.py
efmcalculator/pipeline/mutation_rates.py
efmcalculator/pipeline/post_process.py
efmcalculator/pipeline/primary_pipeline.py
efmcalculator/pipeline/subsequence_curation.py
efmcalculator/webapp/SequenceState.py
efmcalculator/webapp/__init__.py
efmcalculator/webapp/bokeh_plot.py
efmcalculator/webapp/bootstrap_streamlit.py
efmcalculator/webapp/vis_utils.py
efmcalculator/webapp/webapp.py
efmcalculator/webapp/assets/favicon.ico
efmcalculator/webapp/assets/html_template.html
efmcalculator/webapp/assets/stylesheet.css
efmcalculator/webapp/assets/tombstone.ai
efmcalculator/webapp/assets/tombstone.svg
examples/1_L6-10_plasmid.gb
examples/2_EColi_CRISPR_Loci.gb
examples/3_pPath-Violacein-native.gb
paper_scripts/modeling/gam_SRS_model.RData
paper_scripts/modeling/gam_model.json
paper_scripts/modeling/gam_model_components.RData
paper_scripts/modeling/minimal_model.R
paper_scripts/modeling/new.py
paper_scripts/modeling/python_model.py
paper_scripts/modeling/test.csv
tests/__init__.py
tests/test.csv
tests/test_efm2.py