Created
October 18, 2018 00:54
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Download Genbank Assembly DB fasta with BioPython
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| import os | |
| import urllib | |
| import xml.etree.ElementTree as ET | |
| from Bio import Entrez | |
| Entrez.email = "jack.kamm@czbiohub.org" | |
| uid = ET.parse(Entrez.esearch(db="assembly", term="GCA_000150765.1")).getroot().find("IdList")[0].text | |
| ftp_path = ET.parse(Entrez.esummary(db="assembly", id=uid)).getroot().find("DocumentSummarySet").find("DocumentSummary").find("FtpPath_GenBank").text | |
| basename = os.path.basename(ftp_path) | |
| fasta_path = os.path.join(ftp_path, basename + "_genomic.fna.gz") | |
| urllib.request.urlretrieve(fasta_path, os.path.basename(fasta_path)) |
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While NCBI entrez tools can fetch fasta files from some db, unfortunately this doesn't work for the assembly db. Instead, we must use the Entrez tools to fetch the ftp URL, and then download with some other tool. Here, I use BioPython as a wrapper around Entrez to extract this ftp path.