├── .coveragerc ├── .editorconfig ├── .gitattributes ├── .github ├── FUNDING.yml ├── ISSUE_TEMPLATE.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── dependabot.yml └── workflows │ ├── codeql-analysis.yml │ ├── publish.yml │ ├── pull_request.yml │ └── push.yml ├── .gitignore ├── AUTHORS.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── HISTORY.md ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── docs ├── Makefile ├── _static │ ├── copy-button.js │ ├── custom.css │ ├── demo.svg │ ├── e1.png │ ├── e2.png │ ├── e3.png │ ├── pysradb_v3.png │ └── pysradb_v3.svg ├── authors.md ├── case_studies.md ├── cmdline.md ├── commands.rst ├── conf.py ├── contributing.md ├── history.md ├── index.rst ├── installation.md ├── make.bat ├── modules.rst ├── notebooks ├── notebooks.rst ├── pysradb.rst ├── python-api-usage.md └── quickstart.md ├── notebooks ├── 01.Python-API_demo.ipynb ├── 02.Commandline_download.ipynb ├── 03.ParallelDownload.ipynb ├── 04.SRA_to_fastq_conda.ipynb ├── 05.Downloading_subsets_of_a_project.ipynb ├── 06.Multiple_SRPs.ipynb ├── 07.Query_Search.ipynb ├── 08.PMC_DOI_Identifiers.ipynb ├── 09.Metadata_enrichment.ipynb ├── 11.Parse_Bioscience_Search.ipynb └── README.md ├── pyproject.toml ├── pysradb ├── __init__.py ├── __main__.py ├── cli.py ├── download.py ├── exceptions.py ├── filter_attrs.py ├── geoweb.py ├── metadata_enrichment.py ├── ontology_reference.json ├── search.py ├── sraweb.py ├── taxid2name.py └── utils.py ├── requirements.txt ├── setup.cfg └── tests ├── conftest.py ├── data └── test_search │ ├── ena_search_test1.txt │ ├── ena_test_verbosity_0.csv │ ├── ena_test_verbosity_0.json │ ├── ena_test_verbosity_1.csv │ ├── ena_test_verbosity_1.json │ ├── ena_test_verbosity_2.csv │ ├── ena_test_verbosity_2.json │ ├── ena_test_verbosity_3.csv │ ├── ena_test_verbosity_3.json │ ├── geo_search_test1.txt │ ├── sra_search_test1.txt │ ├── sra_test.xml │ ├── sra_test_2_verbosity_0.csv │ ├── 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