50 lines
1.8 KiB
Python
50 lines
1.8 KiB
Python
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from Bio.Blast import NCBIWWW, NCBIXML
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from Bio import SeqIO
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import os
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# Ścieżka do pliku FASTA z sekwencją
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fasta_file = "../data/sequence.fasta"
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# Sprawdzenie, czy plik FASTA istnieje
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if not os.path.exists(fasta_file):
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print("Plik FASTA nie istnieje. Upewnij się, że plik sequence.fasta znajduje się w katalogu data.")
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exit(1)
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# Odczytywanie sekwencji z pliku FASTA
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record = SeqIO.read(fasta_file, format="fasta")
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sequence = str(record.seq)
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# Wykonanie zapytania BLAST
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print("Wysyłanie zapytania BLAST do NCBI...")
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result_handle = NCBIWWW.qblast("blastn", "nt", sequence)
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# Zapis wyników BLAST do pliku XML
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output_file = "../data/blast_results.xml"
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with open(output_file, "w") as out_handle:
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out_handle.write(result_handle.read())
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print(f"Wyniki BLAST zapisane do pliku {output_file}")
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# Parsowanie wyników z pliku XML i wyświetlenie wyników
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print("Analiza wyników BLAST...")
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with open(output_file) as result_handle:
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blast_records = NCBIXML.parse(result_handle)
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for blast_record in blast_records:
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for alignment in blast_record.alignments:
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for hsp in alignment.hsps:
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if hsp.expect < 0.01: # wartość e-value
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print("\n****HIT****")
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print(f"Sequence: {alignment.title}")
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print(f"Length: {alignment.length}")
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print(f"E-value: {hsp.expect}")
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print(f"Score: {hsp.score}")
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print(f"Identities: {hsp.identities}/{hsp.align_length}")
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print("Query sequence:")
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print(hsp.query[0:75] + "...")
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print("Match:")
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print(hsp.match[0:75] + "...")
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print("Subject sequence:")
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print(hsp.sbjct[0:75] + "...")
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