
# PubMed Research Papers CLI Tool

This repository contains a Python CLI tool to fetch research papers from PubMed, identify non-academic authors based on affiliations, and save the results in a CSV file.

## Features

- **Fetch Papers**: Retrieve papers using the PubMed API.
- **Filter Non-Academic Authors**: Identify authors affiliated with non-academic institutions.
- **Command-Line Options**: Flexibility to specify queries, debug mode, and output file.
- **CSV Output**: Save the results in a structured CSV format.

## Requirements

- Python 3.8+

Install package with:

```bash
pip install pubmed_package
```

## Usage

Run the tool from the command line:

```bash
pubmed_api "<query>" [-d] [-f <output_file>]
```

### Arguments

- `<query>`: The search query to use with PubMed.
- `-d, --debug`: Enable debug mode for detailed logs.
- `-f, --file <output_file>`: Specify the filename to save results as CSV. If not provided, results will be printed to the console.

### Example

Fetch papers related to "machine learning" and save them to `results.csv`:

```bash
pubmed_api "breast cancer" -f results.csv
```

Enable debug mode to see detailed execution logs:

```bash
pubmed_api "breast cancer" -d
```

## File Structure

- **pubmed.py**: Main script containing the CLI tool.
- **PubMed_CLI_Tool.ipynb**: Jupyter Notebook version of the script for interactive use.

