LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
bioinformatics_tools/__init__.py
bioinformatics_tools.egg-info/PKG-INFO
bioinformatics_tools.egg-info/SOURCES.txt
bioinformatics_tools.egg-info/dependency_links.txt
bioinformatics_tools.egg-info/entry_points.txt
bioinformatics_tools.egg-info/requires.txt
bioinformatics_tools.egg-info/top_level.txt
bioinformatics_tools/Utilities/__init__.py
bioinformatics_tools/Utilities/command_line.py
bioinformatics_tools/Utilities/warnings.py
bioinformatics_tools/alignmentTools/__init__.py
bioinformatics_tools/alignmentTools/filterBamByReference.py
bioinformatics_tools/alignmentTools/samThresholdFilter.py
bioinformatics_tools/annotationTools/__init__.py
bioinformatics_tools/annotationTools/createVanillaGFF.py
bioinformatics_tools/annotationTools/genbankConverter.py
bioinformatics_tools/annotationTools/genbankToFasta.py
bioinformatics_tools/annotationTools/gff3TEST.py
bioinformatics_tools/annotationTools/gffMine.py
bioinformatics_tools/annotationTools/test.py
bioinformatics_tools/annotationTools/trimGFFByFeature.py
bioinformatics_tools/annotationTools/writeFlaggedContigsNewBinID.py
bioinformatics_tools/annotationTools/writeModeGFFFeaturePerBin.py
bioinformatics_tools/annotationTools/writeTaxonRemovedFastas.py
bioinformatics_tools/api/__init__.py
bioinformatics_tools/api/exceptions.py
bioinformatics_tools/api/main.py
bioinformatics_tools/api/models.py
bioinformatics_tools/api/routers/__init__.py
bioinformatics_tools/api/routers/example.py
bioinformatics_tools/api/routers/fasta.py
bioinformatics_tools/api/routers/ssh_upload.py
bioinformatics_tools/caragols/__init__.py
bioinformatics_tools/caragols/carp.py
bioinformatics_tools/caragols/clix.py
bioinformatics_tools/caragols/condo.py
bioinformatics_tools/caragols/config-template.yaml
bioinformatics_tools/caragols/configurator.py
bioinformatics_tools/caragols/logger.py
bioinformatics_tools/caragols/logging-config.yaml
bioinformatics_tools/caragols/session.py
bioinformatics_tools/fastaTools/FastaClasses.py
bioinformatics_tools/fastaTools/__init__.py
bioinformatics_tools/fastaTools/calcBinsetLengths.py
bioinformatics_tools/fastaTools/combineMultipleFastas.py
bioinformatics_tools/fastaTools/compareTwoBinFiles.py
bioinformatics_tools/fastaTools/fastaToFaa.py
bioinformatics_tools/fastaTools/filterAssembly.py
bioinformatics_tools/fastaTools/genbankConverter.py
bioinformatics_tools/fastaTools/grabEntryDiffs.py
bioinformatics_tools/fastaTools/magBinMatrix.py
bioinformatics_tools/fastaTools/main.py
bioinformatics_tools/fastaTools/newfile.py
bioinformatics_tools/fastaTools/pfamTigrfamProcessingAnvio.py
bioinformatics_tools/fastaTools/revertBinIdToOriginal.py
bioinformatics_tools/fastaTools/splitFastaByHeader.py
bioinformatics_tools/fastaTools/testPrimerSequences.py
bioinformatics_tools/fastaTools/tetranucleotideFreq.py
bioinformatics_tools/fastaTools/writeFastaFromBinID.py
bioinformatics_tools/fastaTools/writeLargestSequences.py
bioinformatics_tools/file_classes/BAM.py
bioinformatics_tools/file_classes/BrowserExtensibleData.py
bioinformatics_tools/file_classes/Fasta.py
bioinformatics_tools/file_classes/Fastq.py
bioinformatics_tools/file_classes/GeneTransferFormat.py
bioinformatics_tools/file_classes/GeneralFeatureFormat.py
bioinformatics_tools/file_classes/Generate.py
bioinformatics_tools/file_classes/__init__.py
bioinformatics_tools/file_classes/base_classes.py
bioinformatics_tools/file_classes/class_skeleton.py
bioinformatics_tools/file_classes/main.py
bioinformatics_tools/misc_tools/__init__.py
bioinformatics_tools/misc_tools/archive_files.py
bioinformatics_tools/misc_tools/cache_clean.py
bioinformatics_tools/misc_tools/extract_files.py
bioinformatics_tools/misc_tools/hello.sh
bioinformatics_tools/misc_tools/hola.sh
bioinformatics_tools/misc_tools/main.py
bioinformatics_tools/misc_tools/slurmfile.py
bioinformatics_tools/misc_tools/test.py
bioinformatics_tools/utilities/__init__.py
bioinformatics_tools/utilities/command_line.py
bioinformatics_tools/utilities/shell_output.py
bioinformatics_tools/utilities/slurm_async_examples.py
bioinformatics_tools/utilities/ssh_slurm.py
bioinformatics_tools/utilities/ssh_slurm_async.py
bioinformatics_tools/utilities/warnings.py
bioinformatics_tools/workflow_tools/bapptainer.py
bioinformatics_tools/workflow_tools/main.py
bioinformatics_tools/workflow_tools/models.py
bioinformatics_tools/workflow_tools/workflow.py
docs/conf.py
tests/__init__.py
tests/conftest.py
tests/test_api.py
tests/test_cli.py
tests/test_clix.py
tests/test_clix_simple.py
tests/test_fasta.py