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docs/advanced.md
docs/index.md
docs/input_format.md
docs/parameters.md
docs/pyproteininference_reference.md
docs/quickstart.md
docs/supplementary.md
docs/img/exclusion.png
docs/img/inclusion.png
docs/img/parsimony.png
docs/img/peptide_centric.jpeg
docs/img/swissprot_example_density.png
parameters/Protein_Inference_Params.yaml
pyproteininference/__init__.py
pyproteininference/datastore.py
pyproteininference/export.py
pyproteininference/heuristic.py
pyproteininference/in_silico_digest.py
pyproteininference/inference.py
pyproteininference/parameters.py
pyproteininference/physical.py
pyproteininference/pipeline.py
pyproteininference/reader.py
pyproteininference/scoring.py
pyproteininference.egg-info/PKG-INFO
pyproteininference.egg-info/SOURCES.txt
pyproteininference.egg-info/dependency_links.txt
pyproteininference.egg-info/not-zip-safe
pyproteininference.egg-info/pbr.json
pyproteininference.egg-info/requires.txt
pyproteininference.egg-info/top_level.txt
scripts/protein_inference_cli.py
scripts/protein_inference_heuristic_cli.py
tests/__init__.py
tests/test_002_inclusion_pipeline.py
tests/test_003_exclusion_pipeline.py
tests/test_004_gfy_type_no_inference_pipeline.py
tests/test_005_parsimony_pipeline_pulp.py
tests/test_006_peptide_centric_pipeline.py
tests/test_007_peptide_parsing.py
tests/test_008_input_reading.py
tests/test_009_additive_custom_pipeline.py
tests/test_010_multiplicative_custom_pipeline.py
tests/test_011_test_exports.py
tests/test_012_test_pipeline_validation.py
tests/test_013_test_datastore_methods.py
tests/test_014_score_methods.py
tests/test_015_digest.py
tests/test_016_faulty_database.py
tests/test_017_missing_database_pipeline.py
tests/test_018_no_alt_proteins_db_recovery.py
tests/test_019_custom_score_restrict.py
tests/test_020_parsimony_pipeline_pulp_none_type_params.py
tests/test_021_parsimony_shared_peptides_assignment.py
tests/test_022_alt_protein_test.py
tests/test_023_malformed_parameters.py
tests/test_024_improper_method_calls.py
tests/test_025_heuristic_pipeline.py
tests/test_026_mapping_recovery.py
tests/test_027_reading_alt_proteins_from_input.py
tests/data/test_data_many_alternative_proteins.txt
tests/data/test_database.fasta
tests/data/test_database_missing_peptide.fasta
tests/data/test_database_missing_protein.fasta
tests/data/test_params_additive_custom_score.yaml
tests/data/test_params_exclusion.yaml
tests/data/test_params_heuristic.yaml
tests/data/test_params_inclusion.yaml
tests/data/test_params_multiplicative_custom_score.yaml
tests/data/test_params_no_inference.yaml
tests/data/test_params_parsimony_pulp.yaml
tests/data/test_params_parsimony_pulp_none_types.yaml
tests/data/test_params_peptide_centric.yaml
tests/data/test_params_slim.yaml
tests/data/test_perc_data_decoy.txt
tests/data/test_perc_data_decoy_additive.txt
tests/data/test_perc_data_decoy_multiplicative.txt
tests/data/test_perc_data_decoy_no_alt_prot.txt
tests/data/test_perc_data_target.txt
tests/data/test_perc_data_target_additive.txt
tests/data/test_perc_data_target_multiplicative.txt
tests/data/test_perc_data_target_no_alt_prot.txt
tests/data/combined_files/test_combined_data.txt
tests/output/all/test_additive_q_value_all_add_example_additive_score.csv
tests/output/all/test_exclusion_q_value_all_ml_posterior_error_prob.csv
tests/output/all/test_inclusion_q_value_all_ml_posterior_error_prob.csv
tests/output/all/test_multiplicative_q_value_all_ml_example_multiplicative_score.csv
tests/output/all/test_no_inference_q_value_all_ml_posterior_error_prob.csv
tests/output/all/test_parsimony_no_grouping_q_value_all_ml_posterior_error_prob.csv
tests/output/all/test_parsimony_q_value_all_ml_posterior_error_prob.csv
tests/output/all/test_parsimony_subset_peptides_q_value_all_ml_posterior_error_prob.csv
tests/output/all/test_peptide_centric_q_value_all_ml_posterior_error_prob.csv
tests/output/leads/test_additive_q_value_leads_add_example_additive_score.csv
tests/output/leads/test_exclusion_q_value_leads_ml_posterior_error_prob.csv
tests/output/leads/test_inclusion_q_value_leads_ml_posterior_error_prob.csv
tests/output/leads/test_multiplicative_q_value_leads_ml_example_multiplicative_score.csv
tests/output/leads/test_no_inference_q_value_leads_ml_posterior_error_prob.csv
tests/output/leads/test_parsimony_no_grouping_q_value_leads_ml_posterior_error_prob.csv
tests/output/leads/test_parsimony_q_value_leads_ml_posterior_error_prob.csv
tests/output/leads/test_parsimony_subset_peptides_q_value_leads_ml_posterior_error_prob.csv
tests/output/leads/test_peptide_centric_q_value_leads_ml_posterior_error_prob.csv
tests/output/peptides/test_additive_q_value_leads_peptides_add_example_additive_score.csv
tests/output/peptides/test_exclusion_q_value_leads_peptides_ml_posterior_error_prob.csv
tests/output/peptides/test_inclusion_q_value_leads_peptides_ml_posterior_error_prob.csv
tests/output/peptides/test_multiplicative_q_value_leads_peptides_ml_example_multiplicative_score.csv
tests/output/peptides/test_no_inference_q_value_leads_peptides_ml_posterior_error_prob.csv
tests/output/peptides/test_parsimony_no_grouping_q_value_leads_peptides_ml_posterior_error_prob.csv
tests/output/peptides/test_parsimony_q_value_leads_peptides_ml_posterior_error_prob.csv
tests/output/peptides/test_parsimony_subset_peptides_q_value_leads_peptides_ml_posterior_error_prob.csv
tests/output/peptides/test_peptide_centric_q_value_leads_peptides_ml_posterior_error_prob.csv
tests/output/psm_ids/test_additive_q_value_leads_psm_ids_add_example_additive_score.csv
tests/output/psm_ids/test_exclusion_q_value_leads_psm_ids_ml_posterior_error_prob.csv
tests/output/psm_ids/test_inclusion_q_value_leads_psm_ids_ml_posterior_error_prob.csv
tests/output/psm_ids/test_multiplicative_q_value_leads_psm_ids_ml_example_multiplicative_score.csv
tests/output/psm_ids/test_no_inference_q_value_leads_psm_ids_ml_posterior_error_prob.csv
tests/output/psm_ids/test_parsimony_no_grouping_q_value_leads_psm_ids_ml_posterior_error_prob.csv
tests/output/psm_ids/test_parsimony_q_value_leads_psm_ids_ml_posterior_error_prob.csv
tests/output/psm_ids/test_parsimony_subset_peptides_q_value_leads_psm_ids_ml_posterior_error_prob.csv
tests/output/psm_ids/test_peptide_centric_q_value_leads_psm_ids_ml_posterior_error_prob.csv
tests/output/psms/test_additive_q_value_leads_psms_add_example_additive_score.csv
tests/output/psms/test_exclusion_q_value_leads_psms_ml_posterior_error_prob.csv
tests/output/psms/test_inclusion_q_value_leads_psms_ml_posterior_error_prob.csv
tests/output/psms/test_multiplicative_q_value_leads_psms_ml_example_multiplicative_score.csv
tests/output/psms/test_no_inference_q_value_leads_psms_ml_posterior_error_prob.csv
tests/output/psms/test_parsimony_no_grouping_q_value_leads_psms_ml_posterior_error_prob.csv
tests/output/psms/test_parsimony_q_value_leads_psms_ml_posterior_error_prob.csv
tests/output/psms/test_parsimony_subset_peptides_q_value_leads_psms_ml_posterior_error_prob.csv
tests/output/psms/test_peptide_centric_q_value_leads_psms_ml_posterior_error_prob.csv