Bio Utils

A lightweight Python package for bioinformatics tasks, designed for educational purposes. The project demonstrates clean Python code, object-oriented programming, and practical usage of third-party bioinformatics libraries.

Features

Biological Sequences (OOP)

• Object-oriented representation of biological sequences
• Abstract base class BiologicalSequence defining a common interface
• DNA and RNA sequences implemented via inheritance and polymorphism
• Protein (amino acid) sequences with domain-specific methods

Supported operations:

• Length calculation (len(sequence))
• Indexing and slicing
• Pretty string representation
• Alphabet validation
• DNA/RNA complement, reverse, and reverse-complement
• DNA transcription into RNA

FASTQ Filtering (Biopython)

• FASTQ filtering using Biopython (SeqIO, SeqRecord, SeqUtils)
• Filtering by:
  • Sequence length
  • GC content (fraction)
  • Mean Phred quality score

FASTA Processing

• Convert multiline FASTA files into single-line FASTA format

BLAST Output Parsing

• Parse BLAST text output
• Extract unique top-hit protein names
• Sort results alphabetically

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Requirements

• Python 3.9+
• Biopython

Install dependencies with:

pip install -r requirements.txt