BioFetcher 0.1.1

A package to download PDB and EMDB files and process protein/map data

BioFetcher

BioFetcher is a Python package that allows you to download bioinformatics data, including PDB, FASTA, and EMDB files. It also includes utilities to extract resolutions for EMDB data and check if a PDB file corresponds to a protein structure.

Features

• Download PDB files from the RCSB Protein Data Bank.
• Download FASTA files associated with PDB entries.
• Download EMDB map files from the Electron Microscopy Data Bank (EMDB).
• Extract the resolution of an EMDB map.
• Check if a PDB file is a protein structure.

Installation

pip install BioFetcher

Installation - from source codes

1. Clone this repository:

   git clone https://github.com/chenwei-zhang/BioFetcher.git
   cd BioFetcher
   

2. Install the package:

   pip install .
   

Python Import

Once you have installed the package, you can import and use the functions in your own Python scripts or projects.

Importing Functions

Here’s how to import the key functions from the BioFetcher package:

from BioFetcher import BioDownloader, extract_res, is_protein_structure

Example Usage in Python

You can use the BioDownloader class to download PDB, FASTA, and EMDB files, or use the helper functions to extract EMDB resolution or check if a PDB corresponds to a protein structure.

# Example of using BioDownloader in Python
downloader = BioDownloader(download_path='.', verbose=True)

# Download PDB and FASTA files
downloader.download_pdb('1abc')
downloader.download_fasta('1abc')

# Check if PDB corresponds to a protein structure
is_protein = is_protein_structure('1abc.pdb')
print(f'Is protein structure: {is_protein}')

# Download EMDB file and extract resolution
downloader.download_emdb('1234')
resolution = extract_res('1234')
print(f'Resolution for EMDB 1234: {resolution}')

Functions

extract_res(emdb_id)

Extracts the resolution value of the EMDB entry with the given ID.

is_protein_structure(pdb_file_path)

Checks if the downloaded PDB file corresponds to a protein structure.

Command-Line Usage

You can run BioFetcher from the command line to download files based on the PDB and EMDB IDs, and specify the download path.

Command-Line Arguments

• --pdb <PDB_ID>: Download the PDB file associated with the specified PDB ID.
• --fasta <PDB_ID>: Download the FASTA file associated with the specified PDB ID.
• --emdb <EMDB_ID>: Download the EMDB map file associated with the specified EMDB ID.
• --download_path <path>: Specify the directory to save the downloaded files (default is the current directory).

Example Usage

• To download a PDB file and its associated FASTA file:

  biofetcher --pdb 1abc --fasta 1abc --download_path /path/to/save/files
  

• To download an EMDB map

  biofetcher --emdb 1234 --download_path /path/to/save/files
  

• To download all files for a specific PDB and EMDB ID:

  biofetcher --pdb 1abc --fasta 1abc --emdb 1234 --download_path /path/to/save/files
  

License

This project is licensed under the GNU License - see the LICENSE file for details.

Support

Chenwei Zhang, [e-mail]