MANIFEST.in
PGGT流程原理.md
README.md
pyproject.toml
src/pggt/__init__.py
src/pggt/cli.py
src/pggt.egg-info/PKG-INFO
src/pggt.egg-info/SOURCES.txt
src/pggt.egg-info/dependency_links.txt
src/pggt.egg-info/entry_points.txt
src/pggt.egg-info/requires.txt
src/pggt.egg-info/top_level.txt
src/pggt/workflow/__init__.py
src/pggt/workflow/run_PGGT.sh
src/pggt/workflow/validate_pipeline_tables.py
src/pggt/workflow/lib/__init__.py
src/pggt/workflow/lib/artifacts.sh
src/pggt/workflow/lib/miniprot_cache.sh
src/pggt/workflow/modules/__init__.py
src/pggt/workflow/modules/allele_cnv_pav/__init__.py
src/pggt/workflow/modules/allele_cnv_pav/build_allele_cnv_pav_table.py
src/pggt/workflow/modules/allele_cnv_pav/make_w_gfa_from_allele_table.py
src/pggt/workflow/modules/allele_cnv_pav/run_allele_cnv_pav_module.sh
src/pggt/workflow/modules/component_filter/01_parse_component_table.py
src/pggt/workflow/modules/component_filter/02_extract_longest_proteins_and_structure.py
src/pggt/workflow/modules/component_filter/03_filter_diamond_hits_to_component_pairs.py
src/pggt/workflow/modules/component_filter/04_score_and_filter_edges.py
src/pggt/workflow/modules/component_filter/05_build_filtered_component_table.py
src/pggt/workflow/modules/component_filter/06_summarize_filter_result.py
src/pggt/workflow/modules/component_filter/__init__.py
src/pggt/workflow/modules/component_filter/run_diamond_structure_filter.sh
src/pggt/workflow/modules/graph/2.segment-pos-threaded-lowmem.py
src/pggt/workflow/modules/graph/3.gene-segment-pos-by-coordinate.py
src/pggt/workflow/modules/graph/4.query-segment-find-ref-segment.strict.py
src/pggt/workflow/modules/graph/__init__.py
src/pggt/workflow/modules/graph/build_noref_gene_components.py
src/pggt/workflow/modules/graph/fast_extract_w_segments_and_s_parallel.py
src/pggt/workflow/modules/graph/run_graph_mapping_allgenome_noref.sh
src/pggt/workflow/modules/singleton_cnv/__init__.py
src/pggt/workflow/modules/singleton_cnv/annotate_singleton_orthogroup_v4.py
src/pggt/workflow/modules/singleton_cnv/build_singleton_joint_evidence_v4.py
src/pggt/workflow/modules/singleton_cnv/build_singleton_orthogroup_table_v2.py
src/pggt/workflow/modules/singleton_cnv/build_singleton_orthogroup_table_v3.py
src/pggt/workflow/modules/singleton_cnv/prepare_singleton_cnv_input.py
src/pggt/workflow/modules/singleton_cnv/prepare_singleton_miniprot_queries_v4.py
src/pggt/workflow/modules/singleton_cnv/run_singleton_orthogroup_miniprot_pfam_v5.sh
src/pggt/workflow/modules/singleton_score/__init__.py
src/pggt/workflow/modules/singleton_score/run_singleton_score_v2.sh
src/pggt/workflow/modules/singleton_score/singleton_score_pipeline.py
tests/test_artifact_retention_and_cache.py
tests/test_coordinate_conventions.py
tests/test_module5_allele_cnv_pav.py
tests/test_package_cli.py
tests/test_parallel_processing.py
tests/test_singleton_score_nocoding.py