39 lines
1.3 KiB
Python
39 lines
1.3 KiB
Python
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from Bio import Entrez, SeqIO
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import os
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# Konfiguracja email dla Entrez (wymagane przez NCBI)
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Entrez.email = "baiobelfer@gmail.com"
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# Identyfikatory GenBank dla wybranych izolatów Fusarium solani
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genbank_ids = [
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"217314860", # Fusarium solani isolate T03
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"2813891763", # Fusarium solani isolate Fso2
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"599088294", # Uncultured Fusarium clone TTRK-10
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"2813891767", # Fusarium solani isolate Fso6
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"2187833333" # Fusarium solani isolate CBG103
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]
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# Katalog do zapisu plików FASTA
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data_dir = "../data"
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os.makedirs(data_dir, exist_ok=True)
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# Funkcja do pobierania genomów i zapisywania ich w plikach FASTA
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def download_genome(genbank_id):
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try:
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# Pobieranie rekordu z NCBI w formacie FASTA
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with Entrez.efetch(db="nucleotide", id=genbank_id, rettype="fasta", retmode="text") as handle:
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record = SeqIO.read(handle, "fasta")
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# Zapis rekordu do pliku FASTA w katalogu ../data
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fasta_path = os.path.join(data_dir, f"{genbank_id}.fasta")
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SeqIO.write(record, fasta_path, "fasta")
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print(f"Pobrano i zapisano {genbank_id} do {fasta_path}")
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except Exception as e:
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print(f"Nie udało się pobrać {genbank_id}: {e}")
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# Pobieranie i zapisywanie genomów dla każdego ID
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for genbank_id in genbank_ids:
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download_genome(genbank_id)
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print("Pobieranie zakończone.")
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