https://bioinformaticsonline.com/snippets/view/44524/python-script-to-finds-extact-similar-sequence-between-two-multi-fasta-files? https://bioinformaticsonline.com/snippets/view/44524/python-script-to-finds-extact-similar-sequence-between-two-multi-fasta-files Thu, 02 May 2024 02:54:56 -0500 https://bioinformaticsonline.com/snippets/view/44524/python-script-to-finds-extact-similar-sequence-between-two-multi-fasta-files from Bio.Blast.Applications import NcbiblastnCommandline import os import sys def perform_local_blast(query_file, subject_file, output_file): # Set up the BLAST command with format 6 (tab-delimited) blastn_cline = NcbiblastnCommandline(query=query_file, subject=subject_file, out=output_file, outfmt=6, word_size=16, perc_identity=100) # Run BLAST stdout, stderr = blastn_cline() # Check for errors if stderr: print("Error running BLAST:") print(stderr) def parse_blast_results(output_file): # Parse BLAST results with open(output_file, "r") as result_handle: for line in result_handle: fields = line.strip().split('\t') qseq = fields[0] # Extract the aligned query sequence (qseq) #print("Aligned Query Sequence:", qseq) # Print other relevant information if needed def main(): if len(sys.argv) != 4: print("Usage: python script.py query.fasta subject.fasta output.txt") sys.exit(1) query_file = sys.argv[1] subject_file = sys.argv[2] output_file = sys.argv[3] # Perform local BLAST perform_local_blast(query_file, subject_file, output_file) # Parse and print BLAST results #parse_blast_results(output_file) if __name__ == "__main__": main()]]> LEGE