https://github.com/berraylvc/bioseq-analyzer

DNA FASTA sequence analyzer built with Biopython
https://github.com/berraylvc/bioseq-analyzer

bioinformatics biopython cli fasta python sequence-analysis

Last synced: 8 days ago
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DNA FASTA sequence analyzer built with Biopython

• Host: GitHub
• URL: https://github.com/berraylvc/bioseq-analyzer
• Owner: berraylvc
• License: mit
• Created: 2025-12-21T23:51:06.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2025-12-23T08:34:30.000Z (5 months ago)
• Last Synced: 2025-12-23T11:20:37.334Z (5 months ago)
• Topics: bioinformatics, biopython, cli, fasta, python, sequence-analysis
• Language: Python
• Homepage:
• Size: 20.5 KB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

          
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# BioSeq Analyzer

A small DNA FASTA sequence analyzer I built while learning basic bioinformatics workflows with **Biopython**.

It reads FASTA files and prints a short report (length, GC%, base counts, transcription/translation previews).

It can also export results to **JSON** and **CSV**.

## What it does

- Parse DNA FASTA files (Biopython `SeqIO`)

- Base counts: A/C/G/T/N (+ common IUPAC ambiguity codes if present)

- GC%, AT%, N%

- mRNA preview (T → U)

- Reverse complement preview

- Protein translation previews (frames 1/2/3)

- CLI tool: `bioseq`

- Unit tests + GitHub Actions CI

## Quickstart (Windows)

    python -m venv .venv

    .\.venv\Scripts\activate

    pip install -e .

    pip install pytest

Run on the example file:

    bioseq --all --json report.json --csv report.csv

Run tests:

    pytest -q

## Quickstart (Linux / macOS)

    python3 -m venv .venv

    source .venv/bin/activate

    pip install -e .

    pip install pytest

## Usage

Analyze a FASTA file:

    bioseq path\to\your.fasta --all

See all options:

    bioseq --help

## Output example

    --- BioSeq Analyzer Report ---

    Record ID        : Example_DNA_1

    Length           : 39 bp

    GC%              : 56.41

    Counts           : {'A': 9, 'C': 8, 'G': 14, 'T': 8, 'N': 0}

    Protein f1 (20)  : MAIVMGR*KGAR*

    -----------------------------

## Notes / Limitations

- This is a learning project (not a full bioinformatics pipeline).

- Large FASTA files may take time because records are currently loaded into memory.

- If sequence length is not a multiple of 3, Biopython may warn about partial codons.

## Project structure

    src/bioseq_analyzer/   # package code

    tests/                 # pytest tests

    data/                  # sample fasta

## Docs

- API notes: `docs/API.md`

- Troubleshooting: `docs/TROUBLESHOOTING.md`

## License

MIT — see `LICENSE`.

## Author

Berra Özyalvaç (GitHub: `@berraylvc`)