LICENSE
README.md
pyproject.toml
setup.cfg
src/pdm_utils/__init__.py
src/pdm_utils/__main__.py
src/pdm_utils/run.py
src/pdm_utils.egg-info/PKG-INFO
src/pdm_utils.egg-info/SOURCES.txt
src/pdm_utils.egg-info/dependency_links.txt
src/pdm_utils.egg-info/entry_points.txt
src/pdm_utils.egg-info/requires.txt
src/pdm_utils.egg-info/top_level.txt
src/pdm_utils/classes/__init__.py
src/pdm_utils/classes/alchemyhandler.py
src/pdm_utils/classes/aragornhandler.py
src/pdm_utils/classes/bundle.py
src/pdm_utils/classes/cds.py
src/pdm_utils/classes/cdspair.py
src/pdm_utils/classes/dbcomparesummary.py
src/pdm_utils/classes/error.py
src/pdm_utils/classes/evaluation.py
src/pdm_utils/classes/fileio.py
src/pdm_utils/classes/filter.py
src/pdm_utils/classes/genome.py
src/pdm_utils/classes/genomepair.py
src/pdm_utils/classes/genometriad.py
src/pdm_utils/classes/progress.py
src/pdm_utils/classes/randomfieldupdatehandler.py
src/pdm_utils/classes/source.py
src/pdm_utils/classes/ticket.py
src/pdm_utils/classes/tmrna.py
src/pdm_utils/classes/trna.py
src/pdm_utils/classes/trnascansehandler.py
src/pdm_utils/constants/__init__.py
src/pdm_utils/constants/constants.py
src/pdm_utils/constants/db_schema_0.py
src/pdm_utils/constants/eval_descriptions.py
src/pdm_utils/constants/schema_conversions.py
src/pdm_utils/functions/__init__.py
src/pdm_utils/functions/annotation.py
src/pdm_utils/functions/basic.py
src/pdm_utils/functions/cartography.py
src/pdm_utils/functions/configfile.py
src/pdm_utils/functions/eval_modes.py
src/pdm_utils/functions/fasta.py
src/pdm_utils/functions/fileio.py
src/pdm_utils/functions/flat_files.py
src/pdm_utils/functions/multiprocess.py
src/pdm_utils/functions/multithread.py
src/pdm_utils/functions/mysqldb.py
src/pdm_utils/functions/mysqldb_basic.py
src/pdm_utils/functions/ncbi.py
src/pdm_utils/functions/parsing.py
src/pdm_utils/functions/phagesdb.py
src/pdm_utils/functions/pham_alignment.py
src/pdm_utils/functions/phameration.py
src/pdm_utils/functions/pipeline_shells.py
src/pdm_utils/functions/pipelines_basic.py
src/pdm_utils/functions/querying.py
src/pdm_utils/functions/rpsblast.py
src/pdm_utils/functions/server.py
src/pdm_utils/functions/subprocess.py
src/pdm_utils/functions/tickets.py
src/pdm_utils/functions/url_basic.py
src/pdm_utils/pipelines/__init__.py
src/pdm_utils/pipelines/compare_db.py
src/pdm_utils/pipelines/convert_db.py
src/pdm_utils/pipelines/export_db.py
src/pdm_utils/pipelines/find_domains.py
src/pdm_utils/pipelines/freeze_db.py
src/pdm_utils/pipelines/get_data.py
src/pdm_utils/pipelines/get_db.py
src/pdm_utils/pipelines/get_gb_records.py
src/pdm_utils/pipelines/import_genome.py
src/pdm_utils/pipelines/pham_finder.py
src/pdm_utils/pipelines/pham_review.py
src/pdm_utils/pipelines/phamerate.py
src/pdm_utils/pipelines/push_db.py
src/pdm_utils/pipelines/revise.py
src/pdm_utils/pipelines/update_field.py