flybasedownloads 4.0.0

Unofficial Python client for downloading and exploring FlyBase datasets.

FlyBase Downloads (FBD)

FlyBase Downloads (FBD) is a lightweight Python library that provides programmatic access to selected datasets from FlyBase, allowing researchers to search, download, and load biological datasets directly into Python objects (e.g. pandas DataFrames) for analysis, exploration, and machine learning workflows.

Important: This is an unofficial library.
All data is retrieved directly from FlyBase, and availability depends entirely on FlyBase’s public resources.

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Purpose

This library is designed for:

• Academic and educational use
• Bioinformatics analysis
• Data exploration in Jupyter notebooks
• Machine learning and data science pipelines

It is not intended for high-frequency or automated bulk downloading.

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Installation and Import

pip install flybasedownloads

from FBD.fbd import FBD

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Basic Usage

List available categories

fbd = FBD()
categories = fbd.get_categories()
print(categories)

List datasets by category

fbd = FBD()
files_by_cat = fbd.get_files_by_category("Genes")
print(files_by_cat)

Search for a dataset (exact or partial match)

Exact match

fbd = FBD()
dataset = fbd.search_file("gene_genetic_interactions")
print("Selected dataset:", dataset)

Partial matches

fbd = FBD()
matches = fbd.search_file("gene")
print("Possible datasets:")
for m in matches:
    print("-", m)

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Download datasets

Initialize with a dataset and download directly

fbd = FBD("gene_genetic_interactions")
df = fbd.download_file()

Download multiple datasets sequentially

fbd = FBD()
fbd.set_dataset("antibody_information")
df1 = fbd.download_file()
fbd.set_dataset("gene_genetic_interactions")
df2 = fbd.download_file()

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Dataset metadata

Retrieve column descriptions

column_info = fbd.get_column_descriptions(
    columns=[
        "Starting_gene(s)_symbol",
        "Ending_gene(s)_symbol",
        "Interaction_type"
    ]
)
print(column_info)

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Example: preparing data for ML

X = df[[
    "Starting_gene(s)_symbol",
    "Ending_gene(s)_symbol"
]]

y = df["Interaction_type"]

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Rate limiting & responsible use

To protect shared infrastructure and respect FlyBase resources, downloads are rate-limited by default. -The download limit is enforced internally -The library is intended for academic use only -Bulk or automated scraping is strongly discouraged

Advanced users can modify the download limits via the Config class and config.json, but: We strongly ask users NOT to bypass rate limits, as this project does not have the infrastructure to support large-scale or abusive usage.

Data source & disclaimer

-All datasets are retrieved directly from FlyBase -This library is not affiliated with FlyBase -Dataset availability may change over time -Some datasets may become unavailable or updated without notice

If you need guaranteed access or bulk data, please use FlyBase’s official distribution channels. Official FlyBase Downloads Overview: FlyBase:Downloads_Overview

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Citation

If you use this library in academic work, please cite FlyBase as the original data source.