"""Basic usage examples for BioPython MCP server."""
from biopython_mcp.alignment import pairwise_align
from biopython_mcp.phylo import build_phylogenetic_tree, draw_tree
from biopython_mcp.sequence import (
calculate_gc_content,
find_motif,
reverse_complement,
transcribe_dna,
translate_sequence,
)
def example_sequence_analysis() -> None:
"""Demonstrate basic sequence analysis."""
print("=== Sequence Analysis Example ===\n")
dna_seq = "ATGGCCATTGTAATGGGCCGC"
print(f"DNA Sequence: {dna_seq}\n")
print("1. Translation:")
result = translate_sequence(dna_seq)
if result["success"]:
print(f" Protein: {result['protein_sequence']}")
print(f" Length: {result['protein_length']} amino acids\n")
print("2. GC Content:")
result = calculate_gc_content(dna_seq)
if result["success"]:
print(f" GC%: {result['gc_content_percent']}%")
print(f" Nucleotide counts: {result['nucleotide_counts']}\n")
print("3. Reverse Complement:")
result = reverse_complement(dna_seq)
if result["success"]:
print(f" Rev Comp: {result['reverse_complement']}\n")
print("4. Transcription:")
result = transcribe_dna(dna_seq)
if result["success"]:
print(f" mRNA: {result['output_sequence']}\n")
print("5. Find Start Codons (ATG):")
result = find_motif(dna_seq, "ATG")
if result["success"]:
print(f" Found {result['occurrences']} occurrences")
print(f" Positions: {result['positions']}\n")
def example_alignment() -> None:
"""Demonstrate sequence alignment."""
print("=== Sequence Alignment Example ===\n")
seq1 = "ATGGCCATTGTAATGGGCCGC"
seq2 = "ATGGCCATTGTTATGGGCCGC"
print(f"Sequence 1: {seq1}")
print(f"Sequence 2: {seq2}\n")
print("Global Alignment:")
result = pairwise_align(seq1, seq2, mode="global")
if result["success"]:
print(f"Score: {result['score']}")
print(f"Alignment:\n{result['alignment']}\n")
print("Local Alignment:")
result = pairwise_align(seq1, seq2, mode="local")
if result["success"]:
print(f"Score: {result['score']}\n")
def example_phylogenetics() -> None:
"""Demonstrate phylogenetic analysis."""
print("=== Phylogenetic Analysis Example ===\n")
sequences = [
"ATGGCCATTGTAATGGGCCGC",
"ATGGCCATTGTTATGGGCCGC",
"ATGGCCATTGTTAAGGGCCGC",
"ATGGCCATTGTTTTGGGCCGC",
]
labels = ["Species_A", "Species_B", "Species_C", "Species_D"]
print("Building phylogenetic tree (Neighbor-Joining)...")
result = build_phylogenetic_tree(sequences, method="nj", labels=labels)
if result["success"]:
print(f"Tree (Newick format):\n{result['tree_newick']}\n")
print("Drawing tree:")
tree_result = draw_tree(result["tree_newick"])
if tree_result["success"]:
print(tree_result["visualization"])
def example_motif_search() -> None:
"""Demonstrate motif searching."""
print("=== Motif Search Example ===\n")
sequence = "ATGGAATTCGCCGAATTCTTAATGGCC"
print(f"Sequence: {sequence}\n")
motifs = {
"Start Codon (ATG)": "ATG",
"EcoRI Site (GAATTC)": "GAATTC",
"Stop Codon (TTA)": "TTA",
}
for name, motif in motifs.items():
result = find_motif(sequence, motif, overlapping=True)
if result["success"]:
print(f"{name}:")
print(f" Pattern: {motif}")
print(f" Occurrences: {result['occurrences']}")
print(f" Positions: {result['positions']}\n")
def main() -> None:
"""Run all examples."""
print("\n" + "=" * 60)
print("BioPython MCP - Basic Usage Examples")
print("=" * 60 + "\n")
example_sequence_analysis()
print("\n" + "-" * 60 + "\n")
example_alignment()
print("\n" + "-" * 60 + "\n")
example_phylogenetics()
print("\n" + "-" * 60 + "\n")
example_motif_search()
print("=" * 60)
print("Examples completed!")
print("=" * 60 + "\n")
if __name__ == "__main__":
main()
