bio_seq Package

Intro

The bioseq package is designed to facilitate bioinformatics operations on DNA, RNA and amino acid sequences and provides a robust object-oriented framework for sequence manipulation.

Features

• Filtering fastq sequences
• Operations on DNA and RNA sequences: transcription, complementation, reversal, reverse complementation, and GC content calculation
• Analysis of aminoacid sequences, including hydrophobicity calculationn

Before usage ensure you have Python installed with the required dependencies (biopython, numpy):

pip install biopython numpy

Usage

Filtering FASTQ Sequences

filtered = filter_fastq("example.fastq", gc_bounds=(40, 60), length_bounds=(50, 150), quality_threshold=20)
if isinstance(filtered, dict):
    for name, (seq, qual) in filtered.items():
        print(f"ID: {name}, Seq: {seq[:10]}..., Quality: {qual[:10]}...")
else:
    print(filtered)
    

DNA/RNA operations

from bio_seq import DNASequence, RNASequence

# DNA example
dna = DNASequence("GATTACA")
print(dna)                    # GATTACA
print(dna.complement())       # CTAATGT
print(dna.reverse())          # ACATTAG
print(dna.reverse_complement()) # TGTAATC
print(dna.count_gc())         # 28.57
rna = dna.transcribe()
print(rna)                    # GAUUACA

# RNA example
rna = RNASequence("AUGCGU")
print(rna)                    # AUGCGU
print(rna.complement())       # UACGCU

Aminoacid operations

from bio_seq import AminoAcidSequence

protein = AminoAcidSequence("MILVFW")
print(protein)                    # MILVFW
print(protein.calculate_hydrophobicity())  # 2.72

Conclusion

This bio_seq package now based an OOP approach, making bioinformatics analyses more modular and extensible nevertheless it can be enhanced with additional functionalities and more advanced features as needed.

P.S.S.

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