.coveragerc
.gitignore
.readthedocs.yml
AUTHORS.rst
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE.txt
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
script_test/evidence_profiler.sh
script_test/get_gen_features_test.sh
script_test/get_sorted_profs.sh
script_test/paco_tranlator_script_test.sh
script_test/profiles2phenopacket_script_test.sh
script_test/expected/get_gen_features/patients_ensemble.txt
script_test/expected/get_gen_features/patients_geneName.txt
script_test/expected/get_gen_features/single_case_ensemble.txt
script_test/expected/get_gen_features/single_case_geneName.txt
script_test/expected/paco_translator/translated_default_file.txt
script_test/expected/paco_translator/translated_paco_file.txt
script_test/expected/paco_translator/untranslated_default_file.txt
script_test/expected/paco_translator/untranslated_paco_file.txt
script_test/expected/profiles2phenopacket/132.json
script_test/expected/profiles2phenopacket/599.json
script_test/expected/profiles2phenopacket/647.json
script_test/expected/profiles2phenopacket/648.json
script_test/input_data/evidence_profiler/get_data.sh
script_test/input_data/evidence_profiler/processed_data/gene_coordinates
script_test/input_data/evidence_profiler/processed_data/gene_coordinates_clean
script_test/input_data/evidence_profiler/processed_data/gene_list
script_test/input_data/evidence_profiler/processed_data/gene_phenotype
script_test/input_data/evidence_profiler/raw_data/gene_phenotype.all.tsv.gz
script_test/input_data/evidence_profiler/raw_data/profile
script_test/input_data/evidence_profiler/raw_data/variant_phenotype.all.tsv.gz
script_test/input_data/evidence_profiler/raw_data/variants/pat_174.tab
script_test/input_data/evidence_profiler/raw_data/variants/pat_174_raw
script_test/input_data/get_gene_features/one_patient_one_feature.txt
script_test/input_data/get_sorted_profs/pmm2_paco_format.txt
script_test/input_data/get_sorted_profs/profile
script_test/input_data/paco_translator/cohort_toy_dataset.txt
script_test/returned/profiles2phenopacket/132.json
script_test/returned/profiles2phenopacket/599.json
script_test/returned/profiles2phenopacket/647.json
script_test/returned/profiles2phenopacket/648.json
src/pets/__init__.py
src/pets/cli_manager.py
src/pets/cohort.py
src/pets/cohort_analyser_methods.py
src/pets/genomic_features.py
src/pets/io.py
src/pets/pets.py
src/pets/external_data/chromosome_sizes_hg18.txt
src/pets/external_data/chromosome_sizes_hg19.txt
src/pets/external_data/chromosome_sizes_hg38.txt
src/pets/external_data/disorder_classes
src/pets/external_data/gencode.v43.basic.annotation.gtf.gz
src/pets/external_data/hp.json
src/pets/external_data/mondo.obo
src/pets/external_data/transform.py
src/pets/external_data/uniq_hpo_with_CI.txt
src/pets/parsers/__init__.py
src/pets/parsers/cohort_parser.py
src/pets/parsers/coord_parser.py
src/pets/parsers/file_parser.py
src/pets/parsers/reference_parser.py
src/pets/templates/cluster_report.txt
src/pets/templates/cohort_report.txt
src/pets/templates/evidence_profile.txt
src/pets/templates/patient_report.txt
src/pets/templates/reg2phen_report.txt
src/pets/templates/similarity_matrix.txt
src/py_pets.egg-info/PKG-INFO
src/py_pets.egg-info/SOURCES.txt
src/py_pets.egg-info/dependency_links.txt
src/py_pets.egg-info/entry_points.txt
src/py_pets.egg-info/not-zip-safe
src/py_pets.egg-info/requires.txt
src/py_pets.egg-info/top_level.txt
tests/__init__.py
tests/conftest.py
tests/test_cli_manager.py
tests/test_cohort.py
tests/test_cohort_parser.py
tests/test_coord_parser.py
tests/test_genomic_feature.py
tests/test_reference_parser.py
tests/data/cohort_toy_dataset.txt
tests/data/cohort_toy_dataset_with_wrong_patient_data.txt
tests/data/coords_toy_dataset.txt
tests/data/ref_parser/toy_example.gtf
tests/data/ref_parser/toy_example_compr.gtf.gz
tests/expected/collapse_terms/collapsed_terms
tests/expected/collapse_terms/collapsed_terms_just_leaves
tests/expected/collapse_terms/collapsed_terms_uniq_parents
tests/expected/diseasome_generator/diseasome
tests/expected/diseasome_generator/diseasome_analysis
tests/expected/filter_omim/filtered_morbid_file
tests/expected/get_gen_features/patients_ensemble.txt
tests/expected/get_gen_features/patients_geneName.txt
tests/expected/get_gen_features/single_case_ensemble.txt
tests/expected/get_gen_features/single_case_geneName.txt
tests/expected/paco_translator/translated_default_file.txt
tests/expected/paco_translator/translated_paco_file.txt
tests/expected/paco_translator/untranslated_default_file.txt
tests/expected/paco_translator/untranslated_paco_file.txt
tests/expected/profiles2phenopacket/132.json
tests/expected/profiles2phenopacket/599.json
tests/expected/profiles2phenopacket/647.json
tests/expected/profiles2phenopacket/648.json
tests/input_data/collapse_terms/terms2collapse
tests/input_data/collapse_terms/terms2txt
tests/input_data/diseasome_generator/diseases
tests/input_data/diseasome_generator/diseasome
tests/input_data/evidence_profiler/get_data.sh
tests/input_data/evidence_profiler/processed_data/gene_coordinates
tests/input_data/evidence_profiler/processed_data/gene_coordinates_clean
tests/input_data/evidence_profiler/processed_data/gene_list
tests/input_data/evidence_profiler/processed_data/gene_phenotype
tests/input_data/evidence_profiler/raw_data/gene_phenotype.all.tsv.gz
tests/input_data/evidence_profiler/raw_data/profile
tests/input_data/evidence_profiler/raw_data/variant_phenotype.all.tsv.gz
tests/input_data/evidence_profiler/raw_data/variants/pat_174.tab
tests/input_data/evidence_profiler/raw_data/variants/pat_174_raw
tests/input_data/filter_omim/morbidmap.txt
tests/input_data/get_gene_features/one_patient_one_feature.txt
tests/input_data/get_sorted_profs/pmm2_paco_format.txt
tests/input_data/get_sorted_profs/profile
tests/input_data/paco_translator/cohort_toy_dataset.txt
tests/tmp/profile_evaluation/file.csv