.appveyor.yml
.codeclimate.yml
.codecov.yml
.coveragerc
.readthedocs.yml
.travis.yml
AUTHORS.rst
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE
MANIFEST.in
README.rst
requirements-rtfd.txt
requirements.txt
setup.cfg
setup.py
tox.ini
docs/Makefile
docs/source/conf.py
docs/source/constants.rst
docs/source/cookbook.rst
docs/source/datamodel.rst
docs/source/dsl.rst
docs/source/examples.rst
docs/source/filters.rst
docs/source/grouping.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/io.rst
docs/source/logging.rst
docs/source/manager.rst
docs/source/models.rst
docs/source/overview.rst
docs/source/parser.rst
docs/source/pipeline.rst
docs/source/postmortem.rst
docs/source/roadmap.rst
docs/source/summary.rst
docs/source/technology.rst
docs/source/transformations.rst
docs/source/troubleshooting.rst
docs/source/utilities.rst
src/PyBEL.egg-info/PKG-INFO
src/PyBEL.egg-info/SOURCES.txt
src/PyBEL.egg-info/dependency_links.txt
src/PyBEL.egg-info/entry_points.txt
src/PyBEL.egg-info/requires.txt
src/PyBEL.egg-info/top_level.txt
src/pybel/__init__.py
src/pybel/__main__.py
src/pybel/canonicalize.py
src/pybel/cli.py
src/pybel/constants.py
src/pybel/exceptions.py
src/pybel/language.py
src/pybel/tokens.py
src/pybel/utils.py
src/pybel/dsl/__init__.py
src/pybel/dsl/edges.py
src/pybel/dsl/exc.py
src/pybel/dsl/namespaces.py
src/pybel/dsl/nodes.py
src/pybel/dsl/utils.py
src/pybel/examples/__init__.py
src/pybel/examples/braf_example.py
src/pybel/examples/egf_example.py
src/pybel/examples/homology_example.py
src/pybel/examples/sialic_acid_example.py
src/pybel/examples/statin_example.py
src/pybel/io/__init__.py
src/pybel/io/cx.py
src/pybel/io/exc.py
src/pybel/io/extras.py
src/pybel/io/gpickle.py
src/pybel/io/indra.py
src/pybel/io/jgif.py
src/pybel/io/line_utils.py
src/pybel/io/lines.py
src/pybel/io/ndex_utils.py
src/pybel/io/neo4j.py
src/pybel/io/nodelink.py
src/pybel/io/utils.py
src/pybel/io/web.py
src/pybel/manager/__init__.py
src/pybel/manager/base_manager.py
src/pybel/manager/cache_manager.py
src/pybel/manager/citation_utils.py
src/pybel/manager/database_io.py
src/pybel/manager/defaults.py
src/pybel/manager/exc.py
src/pybel/manager/lookup_manager.py
src/pybel/manager/make_json_serializable.py
src/pybel/manager/models.py
src/pybel/manager/query_manager.py
src/pybel/manager/utils.py
src/pybel/parser/__init__.py
src/pybel/parser/baseparser.py
src/pybel/parser/exc.py
src/pybel/parser/parse_bel.py
src/pybel/parser/parse_control.py
src/pybel/parser/parse_identifier.py
src/pybel/parser/parse_metadata.py
src/pybel/parser/utils.py
src/pybel/parser/modifiers/__init__.py
src/pybel/parser/modifiers/constants.py
src/pybel/parser/modifiers/fragment.py
src/pybel/parser/modifiers/fusion.py
src/pybel/parser/modifiers/gene_modification.py
src/pybel/parser/modifiers/gene_substitution.py
src/pybel/parser/modifiers/location.py
src/pybel/parser/modifiers/protein_modification.py
src/pybel/parser/modifiers/protein_substitution.py
src/pybel/parser/modifiers/truncation.py
src/pybel/parser/modifiers/variant.py
src/pybel/resources/__init__.py
src/pybel/resources/constants.py
src/pybel/resources/document.py
src/pybel/resources/exc.py
src/pybel/resources/utils.py
src/pybel/resources/definitions/__init__.py
src/pybel/resources/definitions/annotation.py
src/pybel/resources/definitions/definitions.py
src/pybel/resources/definitions/namespace.py
src/pybel/resources/definitions/write_utils.py
src/pybel/struct/__init__.py
src/pybel/struct/graph.py
src/pybel/struct/operations.py
src/pybel/struct/utils.py
src/pybel/struct/filters/__init__.py
src/pybel/struct/filters/edge_filters.py
src/pybel/struct/filters/edge_predicate_builders.py
src/pybel/struct/filters/edge_predicates.py
src/pybel/struct/filters/node_filters.py
src/pybel/struct/filters/node_predicate_builders.py
src/pybel/struct/filters/node_predicates.py
src/pybel/struct/filters/node_selection.py
src/pybel/struct/filters/utils.py
src/pybel/struct/grouping/__init__.py
src/pybel/struct/grouping/annotations.py
src/pybel/struct/grouping/utils.py
src/pybel/struct/mutation/__init__.py
src/pybel/struct/mutation/bound.py
src/pybel/struct/mutation/metadata.py
src/pybel/struct/mutation/transfer.py
src/pybel/struct/mutation/utils.py
src/pybel/struct/mutation/collapse/__init__.py
src/pybel/struct/mutation/collapse/central_dogma.py
src/pybel/struct/mutation/collapse/collapse.py
src/pybel/struct/mutation/deletion/__init__.py
src/pybel/struct/mutation/deletion/central_dogma.py
src/pybel/struct/mutation/deletion/deletion.py
src/pybel/struct/mutation/expansion/__init__.py
src/pybel/struct/mutation/expansion/neighborhood.py
src/pybel/struct/mutation/expansion/upstream.py
src/pybel/struct/mutation/induction/__init__.py
src/pybel/struct/mutation/induction/upstream.py
src/pybel/struct/mutation/inference/__init__.py
src/pybel/struct/mutation/inference/central_dogma.py
src/pybel/struct/pipeline/__init__.py
src/pybel/struct/pipeline/decorators.py
src/pybel/struct/pipeline/exc.py
src/pybel/struct/pipeline/pipeline.py
src/pybel/struct/summary/__init__.py
src/pybel/struct/summary/edge_summary.py
src/pybel/struct/summary/errors.py
src/pybel/struct/summary/node_summary.py
src/pybel/struct/summary/provenance.py
src/pybel/testing/__init__.py
src/pybel/testing/cases.py
src/pybel/testing/constants.py
src/pybel/testing/mocks.py
src/pybel/testing/utils.py
src/pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json
src/pybel/testing/resources/bel/isolated.bel
src/pybel/testing/resources/bel/misordered.bel
src/pybel/testing/resources/bel/slushy.bel
src/pybel/testing/resources/bel/test_bel.bel
src/pybel/testing/resources/bel/thorough.bel
src/pybel/testing/resources/belanno/cell-line.belanno
src/pybel/testing/resources/belanno/confidence-1.0.0.belanno
src/pybel/testing/resources/belanno/mesh-diseases.belanno
src/pybel/testing/resources/belanno/species-taxonomy-id.belanno
src/pybel/testing/resources/belanno/test_an_1.belanno
src/pybel/testing/resources/belns/chebi.belns
src/pybel/testing/resources/belns/disease-ontology.belns
src/pybel/testing/resources/belns/go-biological-process.belns
src/pybel/testing/resources/belns/go-cellular-component.belns
src/pybel/testing/resources/belns/hgnc-human-genes.belns
src/pybel/testing/resources/belns/mesh-diseases.belns
src/pybel/testing/resources/belns/test_nocache.belns
src/pybel/testing/resources/belns/test_ns_1.belns
src/pybel/testing/resources/belns/test_ns_1_updated.belns
src/pybel/testing/resources/belns/test_ns_2.belns
src/pybel/testing/resources/belns/test_ns_empty.belns
tests/__init__.py
tests/constants.py
tests/test_canonicalization.py
tests/test_cli.py
tests/test_dsl.py
tests/test_utils.py
tests/test_io/__init__.py
tests/test_io/test_import.py
tests/test_io/test_jgif.py
tests/test_manager/__init__.py
tests/test_manager/test_citation_utils.py
tests/test_manager/test_manager_definitions.py
tests/test_manager/test_manager_drop.py
tests/test_manager/test_manager_graph.py
tests/test_manager/test_manager_model.py
tests/test_manager/test_seeding.py
tests/test_parse/__init__.py
tests/test_parse/test_parse_bel.py
tests/test_parse/test_parse_bel_relations.py
tests/test_parse/test_parse_bel_variants.py
tests/test_parse/test_parse_control.py
tests/test_parse/test_parse_identifier.py
tests/test_parse/test_parse_metadata.py
tests/test_parse/test_parse_utils.py
tests/test_struct/__init__.py
tests/test_struct/test_grouping.py
tests/test_struct/test_struct_graph.py
tests/test_struct/test_struct_operations.py
tests/test_struct/test_struct_pipeline.py
tests/test_struct/test_filters/__init__.py
tests/test_struct/test_filters/test_node_predicate_builders.py
tests/test_struct/test_filters/test_struct_filters.py
tests/test_struct/test_filters/test_struct_node_predicates.py
tests/test_struct/test_summary/__init__.py
tests/test_struct/test_summary/test_errors.py
tests/test_struct/test_summary/test_struct_summary_edges.py
tests/test_struct/test_summary/test_summary_nodes.py
tests/test_struct/test_transformations/__init__.py
tests/test_struct/test_transformations/test_collapse.py
tests/test_struct/test_transformations/test_deletions.py
tests/test_struct/test_transformations/test_expansion.py
tests/test_struct/test_transformations/test_induction.py
tests/test_struct/test_transformations/test_infererence_central_dogma.py
tests/test_struct/test_transformations/test_metadata.py
tests/test_struct/test_transformations/test_transfer.py