.codecov.yml
.gitignore
.lgtm.yml
.travis.yml
CODE_OF_CONDUCT.md
LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
versioneer.py
.github/CONTRIBUTING.md
.github/PULL_REQUEST_TEMPLATE.md
devtools/README.md
devtools/conda-envs/test_env.yaml
devtools/scripts/create_conda_env.py
devtools/travis-ci/before_install.sh
docs/Makefile
docs/README.md
docs/apis.rst
docs/conf.py
docs/domain.rst
docs/examples.rst
docs/index.rst
docs/interfaces.rst
docs/make.bat
docs/overview.rst
docs/protein.rst
docs/proteome.rst
docs/site.rst
docs/track.rst
docs/_static/README.md
docs/_templates/README.md
docs/autosummary/shephard.proteome.rst
shephard/__init__.py
shephard/_version.py
shephard/domain.py
shephard/exceptions.py
shephard/general_utilities.py
shephard/protein.py
shephard/proteome.py
shephard/sequence_utilities.py
shephard/site.py
shephard/test_domains_sites.py
shephard/track.py
shephard.egg-info/PKG-INFO
shephard.egg-info/SOURCES.txt
shephard.egg-info/dependency_links.txt
shephard.egg-info/requires.txt
shephard.egg-info/top_level.txt
shephard/apis/__init__.py
shephard/apis/fasta.py
shephard/apis/uniprot.py
shephard/data/README.md
shephard/data/look_and_say.dat
shephard/data/test_data/TS1_domains_idr.tsv
shephard/data/test_data/TS1_domains_idr_and_others.tsv
shephard/data/test_data/TS1_domains_pscore.tsv
shephard/data/test_data/TS1_protein_attributes.tsv
shephard/data/test_data/TS1_sites.tsv
shephard/data/test_data/TS1_tracks_pscore.tsv
shephard/data/test_data/names.txt
shephard/data/test_data/seqs.fasta
shephard/data/test_data/testset_1.fasta
shephard/data/test_data/testset_1.fasta.fai
shephard/data/test_data/testset_1_ptms.tsv
shephard/data/test_data/ts1_bonus_sites.tsv
shephard/data/test_data/ts1_bonus_sites_bad.tsv
shephard/data/test_data/ts1_bonus_sites_bad2.tsv
shephard/data/test_data/tst.py
shephard/interfaces/__init__.py
shephard/interfaces/interface_tools.py
shephard/interfaces/si_domains.py
shephard/interfaces/si_protein_attributes.py
shephard/interfaces/si_proteins.py
shephard/interfaces/si_sites.py
shephard/interfaces/si_tracks.py
shephard/tests/__init__.py
shephard/tests/conftest.py
shephard/tests/example_test_function.py
shephard/tests/test_add_remove_annotations.py
shephard/tests/test_apis_fasta.py
shephard/tests/test_domain_tools.py
shephard/tests/test_domains.py
shephard/tests/test_interfaces.py
shephard/tests/test_logic.py
shephard/tests/test_protein.py
shephard/tests/test_protein_site_functions.py
shephard/tests/test_proteome.py
shephard/tests/test_scratchpad.ipynb
shephard/tests/test_sequence_tools.py
shephard/tests/test_shephard.py
shephard/tests/test_si_domains.py
shephard/tests/test_si_sites.py
shephard/tests/test_si_tracks.py
shephard/tests/test_sites.py
shephard/tests/test_track_tools.py
shephard/tests/test_tracks.py
shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb
shephard/tests/output_test/all_symbols_test.tsv
shephard/tests/output_test/all_values_test.tsv
shephard/tests/output_test/all_values_test_from_list.tsv
shephard/tests/output_test/out_tracks.tsv
shephard/tests/output_test/readme.md
shephard/tests/output_test/shephard_track_phosres.tsv
shephard/tests/output_test/shephard_track_pscore.tsv
shephard/tests/output_test/test_domains.tsv
shephard/tests/output_test/test_sites.tsv
shephard/tests/output_test/track_phospho_track.tsv
shephard/tests/output_test/track_random_vals.tsv
shephard/tools/__init__.py
shephard/tools/domain_tools.py
shephard/tools/experimental.py
shephard/tools/sequence_tools.py
shephard/tools/site_tools.py
shephard/tools/track_tools.py