Initial commit
This commit is contained in:
Zhongwei Li
191
skills/gget/scripts/batch_sequence_analysis.py
Executable file
191
skills/gget/scripts/batch_sequence_analysis.py
Executable file
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#!/usr/bin/env python3
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"""
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Batch Sequence Analysis Script
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Analyze multiple sequences: BLAST, alignment, and structure prediction
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"""
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import argparse
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import sys
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from pathlib import Path
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import gget
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def read_fasta(fasta_file):
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"""Read sequences from FASTA file."""
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sequences = []
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current_id = None
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current_seq = []
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with open(fasta_file, "r") as f:
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for line in f:
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line = line.strip()
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if line.startswith(">"):
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if current_id:
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sequences.append({"id": current_id, "seq": "".join(current_seq)})
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current_id = line[1:]
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current_seq = []
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else:
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current_seq.append(line)
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if current_id:
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sequences.append({"id": current_id, "seq": "".join(current_seq)})
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return sequences
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def analyze_sequences(
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fasta_file,
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blast_db="nr",
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align=True,
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predict_structure=False,
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output_dir="output",
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):
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"""
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Perform batch sequence analysis.
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Args:
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fasta_file: Path to FASTA file with sequences
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blast_db: BLAST database to search (default: nr)
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align: Whether to perform multiple sequence alignment
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predict_structure: Whether to predict structures with AlphaFold
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output_dir: Output directory for results
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"""
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output_path = Path(output_dir)
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output_path.mkdir(exist_ok=True)
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print(f"Batch Sequence Analysis")
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print("=" * 60)
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print(f"Input file: {fasta_file}")
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print(f"Output directory: {output_dir}")
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print("")
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# Read sequences
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print("Reading sequences...")
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sequences = read_fasta(fasta_file)
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print(f"Found {len(sequences)} sequences\n")
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# Step 1: BLAST each sequence
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print("Step 1: Running BLAST searches...")
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print("-" * 60)
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for i, seq_data in enumerate(sequences):
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print(f"\n{i+1}. BLASTing {seq_data['id']}...")
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try:
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blast_results = gget.blast(
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seq_data["seq"], database=blast_db, limit=10, save=False
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)
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output_file = output_path / f"{seq_data['id']}_blast.csv"
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blast_results.to_csv(output_file, index=False)
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print(f" Results saved to: {output_file}")
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if len(blast_results) > 0:
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print(f" Top hit: {blast_results.iloc[0]['Description']}")
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print(
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f" Max Score: {blast_results.iloc[0]['Max Score']}, "
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f"Query Coverage: {blast_results.iloc[0]['Query Coverage']}"
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)
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except Exception as e:
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print(f" Error: {e}")
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# Step 2: Multiple sequence alignment
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if align and len(sequences) > 1:
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print("\n\nStep 2: Multiple sequence alignment...")
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print("-" * 60)
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try:
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alignment = gget.muscle(fasta_file)
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alignment_file = output_path / "alignment.afa"
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with open(alignment_file, "w") as f:
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f.write(alignment)
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print(f"Alignment saved to: {alignment_file}")
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except Exception as e:
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print(f"Error in alignment: {e}")
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else:
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print("\n\nStep 2: Skipping alignment (only 1 sequence or disabled)")
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# Step 3: Structure prediction (optional)
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if predict_structure:
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print("\n\nStep 3: Predicting structures with AlphaFold...")
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print("-" * 60)
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print(
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"Note: This requires 'gget setup alphafold' and is computationally intensive"
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)
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for i, seq_data in enumerate(sequences):
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print(f"\n{i+1}. Predicting structure for {seq_data['id']}...")
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try:
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structure_dir = output_path / f"structure_{seq_data['id']}"
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# Uncomment to run AlphaFold prediction:
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# gget.alphafold(seq_data['seq'], out=str(structure_dir))
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# print(f" Structure saved to: {structure_dir}")
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print(
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" (Prediction skipped - uncomment code to run AlphaFold prediction)"
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)
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except Exception as e:
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print(f" Error: {e}")
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else:
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print("\n\nStep 3: Structure prediction disabled")
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# Summary
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print("\n" + "=" * 60)
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print("Batch analysis complete!")
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print(f"\nResults saved to: {output_dir}/")
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print(f" - BLAST results: *_blast.csv")
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if align and len(sequences) > 1:
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print(f" - Alignment: alignment.afa")
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if predict_structure:
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print(f" - Structures: structure_*/")
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return True
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def main():
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parser = argparse.ArgumentParser(
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description="Perform batch sequence analysis using gget"
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)
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parser.add_argument("fasta", help="Input FASTA file with sequences")
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parser.add_argument(
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"-db",
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"--database",
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default="nr",
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help="BLAST database (default: nr for proteins, nt for nucleotides)",
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)
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parser.add_argument(
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"--no-align", action="store_true", help="Skip multiple sequence alignment"
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)
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parser.add_argument(
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"--predict-structure",
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action="store_true",
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help="Predict structures with AlphaFold (requires setup)",
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)
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parser.add_argument(
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"-o", "--output", default="output", help="Output directory (default: output)"
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)
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args = parser.parse_args()
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if not Path(args.fasta).exists():
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print(f"Error: File not found: {args.fasta}")
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sys.exit(1)
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try:
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success = analyze_sequences(
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args.fasta,
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blast_db=args.database,
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align=not args.no_align,
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predict_structure=args.predict_structure,
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output_dir=args.output,
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)
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sys.exit(0 if success else 1)
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except KeyboardInterrupt:
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print("\n\nAnalysis interrupted by user")
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sys.exit(1)
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except Exception as e:
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print(f"\n\nError: {e}")
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import traceback
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traceback.print_exc()
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sys.exit(1)
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if __name__ == "__main__":
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main()
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