SNP Info Extractor

A simple Python script that extracts basic SNP (rsID) information from NCBI SNP pages and saves it to an Excel file.
It retrieves chromosome, GRCh37 / GRCh38 positions, alleles, and gene consequence.

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Features

• Input: a comma-separated list of rs IDs (e.g. rs429358, rs7412)
• Output: Excel file with columns: rsID, Chromosome, GRCh37 Position, GRCh38 Position, Alleles, Gene Consequence
• Ideal for small-scale SNP lookups.

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Requirements

• Python 3.8+
• Python packages:

pip install requests beautifulsoup4 pandas openpyxl lxml

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Output Columns

• rsID — SNP identifier
• Chromosome — Chromosome number (if available)
• GRCh37 Position — Numeric position on GRCh37
• GRCh38 Position — Numeric position on GRCh38
• Alleles — Allele string
• Gene Consequence — Consequence or None if missing

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How it Works

1. Fetches NCBI SNP webpage for each rsID: https://www.ncbi.nlm.nih.gov/snp/{rsid}.

2. Uses BeautifulSoup to parse HTML and extract:

   • Position, Alleles, Gene : Consequence
   • Placement table (genomics_placements_table) for GRCh37/GRCh38 coordinates

3. Combines all results in a pandas DataFrame and writes to Excel.

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Important Notes

• The script scrapes NCBI public pages. For large-scale queries, use NCBI Entrez/e-utilities.
• Some fields may be missing for certain SNPs; these will appear blank in Excel.
• Internet connection is required.

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License

This project is licensed under the MIT License. See LICENSE for details.

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Contact / Author

Created by Rahul Madhav