"""Sequence analysis tools using BioPython."""
from typing import Any
from Bio.Seq import Seq
from Bio.SeqUtils import gc_fraction
from biopython_mcp.utils import validate_sequence
def translate_sequence(sequence: str, table: int = 1, to_stop: bool = False) -> dict[str, Any]:
"""
Translate a DNA or RNA sequence to protein.
Args:
sequence: DNA or RNA sequence string
table: Genetic code table to use (default: 1 for standard code)
to_stop: Stop translation at first stop codon (default: False)
Returns:
Dictionary containing the translated protein sequence and metadata
"""
try:
seq = Seq(validate_sequence(sequence))
protein = seq.translate(table=table, to_stop=to_stop)
return {
"success": True,
"input_sequence": str(sequence),
"input_length": len(sequence),
"protein_sequence": str(protein),
"protein_length": len(protein),
"table": table,
"stopped_at_stop_codon": to_stop,
}
except Exception as e:
return {"success": False, "error": str(e), "input_sequence": sequence}
def reverse_complement(sequence: str) -> dict[str, Any]:
"""
Get the reverse complement of a DNA sequence.
Args:
sequence: DNA sequence string
Returns:
Dictionary containing the reverse complement and metadata
"""
try:
seq = Seq(validate_sequence(sequence))
rev_comp = seq.reverse_complement()
return {
"success": True,
"input_sequence": str(sequence),
"reverse_complement": str(rev_comp),
"length": len(sequence),
}
except Exception as e:
return {"success": False, "error": str(e), "input_sequence": sequence}
def transcribe_dna(sequence: str, reverse: bool = False) -> dict[str, Any]:
"""
Transcribe DNA to RNA (or reverse transcribe RNA to DNA).
Args:
sequence: DNA or RNA sequence string
reverse: If True, reverse transcribe RNA to DNA (default: False)
Returns:
Dictionary containing the transcribed sequence and metadata
"""
try:
seq = Seq(validate_sequence(sequence))
if reverse:
result = seq.back_transcribe()
operation = "reverse_transcription"
else:
result = seq.transcribe()
operation = "transcription"
return {
"success": True,
"input_sequence": str(sequence),
"output_sequence": str(result),
"operation": operation,
"length": len(sequence),
}
except Exception as e:
return {"success": False, "error": str(e), "input_sequence": sequence}
def calculate_gc_content(sequence: str) -> dict[str, Any]:
"""
Calculate the GC content of a DNA or RNA sequence.
Args:
sequence: DNA or RNA sequence string
Returns:
Dictionary containing GC content percentage and counts
"""
try:
seq = Seq(validate_sequence(sequence))
gc_percent = gc_fraction(seq) * 100
g_count = sequence.upper().count("G")
c_count = sequence.upper().count("C")
a_count = sequence.upper().count("A")
t_count = sequence.upper().count("T")
u_count = sequence.upper().count("U")
return {
"success": True,
"sequence_length": len(sequence),
"gc_content_percent": round(gc_percent, 2),
"nucleotide_counts": {
"G": g_count,
"C": c_count,
"A": a_count,
"T": t_count,
"U": u_count,
},
"gc_count": g_count + c_count,
"at_count": a_count + t_count,
}
except Exception as e:
return {"success": False, "error": str(e), "sequence": sequence}
def find_motif(sequence: str, motif: str, overlapping: bool = True) -> dict[str, Any]:
"""
Find all occurrences of a motif in a sequence.
Args:
sequence: DNA, RNA, or protein sequence to search
motif: Motif pattern to find
overlapping: Allow overlapping matches (default: True)
Returns:
Dictionary containing motif positions and count
"""
try:
sequence = validate_sequence(sequence)
motif = validate_sequence(motif)
positions = []
start = 0
while True:
pos = sequence.upper().find(motif.upper(), start)
if pos == -1:
break
positions.append(pos)
start = pos + (1 if overlapping else len(motif))
return {
"success": True,
"sequence_length": len(sequence),
"motif": motif,
"motif_length": len(motif),
"occurrences": len(positions),
"positions": positions,
"overlapping_search": overlapping,
}
except Exception as e:
return {"success": False, "error": str(e), "sequence": sequence, "motif": motif}
