.coveragerc
.gitignore
.readthedocs.yml
AUTHORS.rst
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE.txt
MANIFEST.in
README.md
README.rst
pyproject.toml
setup.cfg
setup.py
tox.ini
docs/Makefile
docs/authors.rst
docs/changelog.rst
docs/conf.py
docs/contributing.rst
docs/index.rst
docs/license.rst
docs/readme.rst
docs/requirements.txt
docs/_static/.gitignore
src/py_semtools/__init__.py
src/py_semtools/cli_manager.py
src/py_semtools/main_modules.py
src/py_semtools/ontology.py
src/py_semtools/parallelizer.py
src/py_semtools/report_ont.py
src/py_semtools/sim_handler.py
src/py_semtools.egg-info/PKG-INFO
src/py_semtools.egg-info/SOURCES.txt
src/py_semtools.egg-info/dependency_links.txt
src/py_semtools.egg-info/entry_points.txt
src/py_semtools.egg-info/not-zip-safe
src/py_semtools.egg-info/requires.txt
src/py_semtools.egg-info/top_level.txt
src/py_semtools/external_data/ontologies.txt
src/py_semtools/indexers/text_indexer.py
src/py_semtools/lexical_engines/engine_baseclass.py
src/py_semtools/lexical_engines/fmEngine.py
src/py_semtools/lexical_engines/stEngine.py
src/py_semtools/parsers/ont/file_parser.py
src/py_semtools/parsers/ont/json_parser.py
src/py_semtools/parsers/ont/oboparser.py
src/py_semtools/parsers/text/text_basic_parser.py
src/py_semtools/parsers/text/text_pubmed_abstract_parser.py
src/py_semtools/parsers/text/text_pubmed_paper_parser.py
src/py_semtools/parsers/text/text_pubmed_parser.py
src/py_semtools/templates/comorb_sugg.txt
src/py_semtools/templates/makeTermFreqTable.txt
src/py_semtools/templates/ontoICdist.txt
src/py_semtools/templates/ontodist.txt
src/py_semtools/templates/ontoplot.txt
src/py_semtools/templates/plotClust.txt
src/py_semtools/templates/plotProfRed.txt
src/py_semtools/templates/report.txt
src/py_semtools/templates/similarity_heatmap.txt
src/py_semtools/templates/similarity_matrix.txt
src/py_semtools/templates/stEngine.txt
tests/__init__.py
tests/conftest.py
tests/test_cli_manager.py
tests/test_go.py
tests/test_jsonparser.py
tests/test_oboparser.py
tests/test_ontology.py
tests/test_pubmed_abs_parser.py
tests/test_pubmed_pap_parser.py
tests/test_pubmed_text_parser.py
tests/test_similitudes.py
tests/test_stengine.py
tests/test_text_indexer.py
tests/cli_examples/Report.html
tests/cli_examples/example
tests/cli_examples/launch.sh
tests/cli_examples/styles.css
tests/cli_examples/template.txt
tests/data/branched.obo
tests/data/circular_sample.obo
tests/data/enrichment_ontology.obo
tests/data/enrichment_ontology2.obo
tests/data/enrichment_ontology3.obo
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tests/data/go-onlyOne.obo
tests/data/hierarchical_alt_chain.obo
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tests/data/only_header_sample.obo
tests/data/partial_go.json
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tests/data/get_sorted_profs/report.html
tests/data/get_sorted_profs/report.txt
tests/data/get_sorted_suggestions/expected/filter_query_parentals.txt
tests/data/get_sorted_suggestions/expected/filter_target_and_query_parentals.txt
tests/data/get_sorted_suggestions/expected/filter_target_parentals.txt
tests/data/get_sorted_suggestions/expected/no_filter_limit_2.txt
tests/data/get_sorted_suggestions/expected/no_filter_no_limit.txt
tests/data/get_sorted_suggestions/input_data/enrichment_ontology3.obo
tests/data/get_sorted_suggestions/input_data/query_hps.txt
tests/data/get_sorted_suggestions/input_data/relations.txt
tests/data/input_scripts/profiles
tests/data/input_scripts/profiles_2cols
tests/data/input_scripts/profiles_with_removedTerms
tests/data/input_scripts/string_values
tests/data/input_scripts/terms
tests/data/input_scripts/terms_for_xref
tests/data/input_scripts/terms_list
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tests/data/ref_output_scripts/cleaned_profiles
tests/data/ref_output_scripts/cleaned_profiles_2cols
tests/data/ref_output_scripts/expanded_profiles
tests/data/ref_output_scripts/expected_IC_ont
tests/data/ref_output_scripts/parental_from_terms
tests/data/ref_output_scripts/profile_stats
tests/data/ref_output_scripts/profiles_IC_onto_freq
tests/data/ref_output_scripts/strsimnet
tests/data/ref_output_scripts/strsimnet_cutoff2
tests/data/ref_output_scripts/terms_attr
tests/data/ref_output_scripts/translated_profiles_names
tests/data/ref_output_scripts/translated_terms_codes
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tests/data/stEngine/inputs/blacklisted_words1.txt
tests/data/stEngine/inputs/blacklisted_words2.txt
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tests/data/stEngine/inputs/prepared_indexes/queries/hpo_list
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tests/demo_examples/launch.sh
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tests/demo_examples/profiles_freqs.html
tests/demo_examples/template.txt
tests/demo_examples/data/profiles.txt
tests/demo_examples/data/ref_profile.txt