.coveragerc
.gitignore
CHANGELOG.md
LICENSE
MANIFEST.in
README.md
RELEASE_NOTES_v1.4.0.md
pyproject.toml
pytest.ini
requirements-dev.txt
requirements.txt
setup.py
.github/workflows/tests.yml
distances/distances.hpp
distances/embeding.cpp
distances/thread_wrappers.hpp
distances/trf_file.hpp
scripts/batch_check_trf_consistency.py
scripts/check_telomeres.py
scripts/check_trf_consistency.py
scripts/plots.py
scripts/run_satellome_batch.sh
scripts/run_satellome_parallel.py
scripts/tandems.py
scripts/to_fasta.py
scripts/trf_get_large.py
scripts/trf_get_micro_stat.py
scripts/trf_refine.py
scripts/trf_to_coordinates.py
scripts/trf_to_fasta.py
scripts/trf_to_gff3.py
scripts/trs_set_chrm_names_for_fasta.py
scripts/yaml_parser.py
src/satellome/__init__.py
src/satellome/constants.py
src/satellome/install_command.py
src/satellome/main.py
src/satellome/redraw.py
src/satellome/settings.yaml
src/satellome/trc_set_tr_names_color.py
src/satellome.egg-info/PKG-INFO
src/satellome.egg-info/SOURCES.txt
src/satellome.egg-info/dependency_links.txt
src/satellome.egg-info/entry_points.txt
src/satellome.egg-info/requires.txt
src/satellome.egg-info/top_level.txt
src/satellome/core_functions/__init__.py
src/satellome/core_functions/classification_micro.py
src/satellome/core_functions/exceptions.py
src/satellome/core_functions/settings.py
src/satellome/core_functions/trf_clusters.py
src/satellome/core_functions/trf_drawing.py
src/satellome/core_functions/trf_embedings.py
src/satellome/core_functions/io/__init__.py
src/satellome/core_functions/io/abstract_reader.py
src/satellome/core_functions/io/block_file.py
src/satellome/core_functions/io/fasta_file.py
src/satellome/core_functions/io/file_system.py
src/satellome/core_functions/io/gff_file.py
src/satellome/core_functions/io/tab_file.py
src/satellome/core_functions/io/tr_file.py
src/satellome/core_functions/io/trf_file.py
src/satellome/core_functions/models/__init__.py
src/satellome/core_functions/models/abstract_model.py
src/satellome/core_functions/models/gff3_model.py
src/satellome/core_functions/models/trf_model.py
src/satellome/core_functions/tools/__init__.py
src/satellome/core_functions/tools/bed_tools.py
src/satellome/core_functions/tools/clusterization.py
src/satellome/core_functions/tools/distances.py
src/satellome/core_functions/tools/gene_intersect.py
src/satellome/core_functions/tools/gene_intersect_streaming.py
src/satellome/core_functions/tools/kmer_splitting.py
src/satellome/core_functions/tools/ncbi.py
src/satellome/core_functions/tools/parsers.py
src/satellome/core_functions/tools/processing.py
src/satellome/core_functions/tools/reports.py
src/satellome/core_functions/tools/statistics.py
src/satellome/core_functions/tools/trf_tools.py
src/satellome/core_functions/tools/validation.py
src/satellome/installers/__init__.py
src/satellome/installers/base.py
src/satellome/installers/fastan.py
src/satellome/installers/tanbed.py
src/satellome/installers/trf_large.py
src/satellome/installers/trf_standard.py
src/satellome/steps/__init__.py
src/satellome/steps/trf_classify.py
src/satellome/steps/trf_draw.py
src/satellome/steps/trf_parse_raw.py
src/satellome/steps/trf_search.py
tests/__init__.py
tests/conftest.py
tests/test_fixtures.py
tests/test_gene_intersect_streaming.py
tests/test_validation.py
tests/fixtures/sample_data.py
tests/unit/__init__.py
tests/unit/test_bed_tools.py
tests/unit/test_classification_micro.py
tests/unit/test_parsers.py
tests/unit/test_processing.py
tests/unit/test_trf_model.py
tests/unit/test_trf_tools.py