是否有一种使用Python从NCBI下载fasta格式的基因组的简单方法？

Question

我正在尝试使用Python从NCBI (最好是fasta格式)下载基因组，但是到目前为止没有什么真正的工作。API对我来说是新的，我并不真正理解文档(https://www.ncbi.nlm.nih.gov/books/NBK25497/)。

我的最终目标是下载一个属内每个物种的所有基因组，但是用Python下载一个基因组将是一个很好的开始。

除了使用API之外，我还可以使用其他选项。

(预先谢谢:)

编辑:这是我的代码示例

import ncbi_genome_download as ngd

taxon_name = "Rubus"
ngd.download().group(taxon_name)

这是在古菌群中下载基因组数据，但不是在我感兴趣的组: Rubus。

Answer 1

是的，有这么简单的方法：

from Bio import Entrez

Entrez.email = "your.box@mail.xyz"
Entrez.api_key = "y0ur_ap1_key"

IDs = Entrez.read(Entrez.esearch(db="nucleotide", retmax=3, term="Procyon lotor", field="Organism"))["IdList"]
for ID in IDs:
    print(Entrez.efetch(db="nucleotide", id=ID, rettype="fasta", retmode="text").read())

输出：

>MK804320.1 Procyon lotor voucher MNHN:TC793 cytochrome b (CYTB) gene, partial cds; mitochondrial
GGGCAACAGTAATTACAAACCTCCTGTCAGCTATCCCCTATATCGGATCTAACCTTGTAGAATGAATTTG
AGGAGGGTTTTCAGTAGACAAAGCCACCCTAACACGATTCTTCGCATTCCACTTCATTCTACCATTTATT
ATCACAGCGCTAGCAATAATTCACCTGCTATTCCTACACGAAACAGGATCCAATAACCCTTCTGGAATTA
CATCAGAATCTGACAAAATTCCATTTCACCCATACTACACCATTAAAGACATTCTGGGAATCCTATTCCT
TATTTTTGTACTTATAGGTTTAGTGCTATTTACGCCAGACCTACTAGGTGACCCAGATAATTACACACCC
GCTAACCCCTTAAACACCCCACCTCACATTAAACCTGAATGATATTTTCTATTCGCCTACGCAATTCTAC
GTTCCATTCCCAACAAACTAGGAGGAGTCCTAGCCCTAGTCCTCTCCATCTTAATCCTAATCATCATTCC
ACTCCTACACACCTCAAAACAACGAAGCATAATATTTCGGCCACTTAGCCAATGTTTATTCTGATTCCTA
GTAGCAGACCTCCTCGTCCTAACATGAATTGGAGGTCAACCAGTAGAATATCCCTTCATCATCATCGGCC
AACTAGCCTCCATCTTCTACTTTATAATCCTCCTGATCCTAATACCAACAATAAATATCATCGAAAATAA
TCTGTTAAAATGAAGA


>MK804319.1 Procyon lotor voucher MNHN:TC792 cytochrome b (CYTB) gene, partial cds; mitochondrial
GGGCAACAGTAATTACAAACCTCCTGTCAGCTATCCCCTATATCGGATCTAACCTTGTAGAATGAATTTG
AGGAGGGTTTTCAGTAGACAAAGCCACCCTAACACGATTCTTCGCATTCCACTTCATTCTACCATTTATT
ATCACAGCGCTAGCAATAATTCACCTGCTATTCCTACACGAAACAGGATCCAATAACCCTTCTGGAATTA
CATCAGAATCTGACAAAATTCCATTTCACCCATACTACACCATTAAAGACATTCTGGGAATCCTATTCCT
TATTTTTGTACTTATAGGTTTAGTGCTATTTACGCCAGACCTACTAGGTGACCCAGATAATTACACACCC
GCTAACCCCTTAAACACCCCACCTCACATTAA


>MK804318.1 Procyon lotor voucher MNHN:TC791 cytochrome b (CYTB) gene, partial cds; mitochondrial
GGGCAACAGTAATTACAAACCTCCTGTCAGCTATCCCCTATATCGGATCTAACCTTGTAGAATGAATTTG
AGGAGGGTTTTCAGTAGACAAAGCCACCCTAACACGATTCTTCGCATTCCACTTCATTCTACCATTTATT
ATCACAGCGCTAGCAATAATTCACCTGCTATTCCTACACGAAACAGGATCCAATAACCCTTCTGGAATTA
CATCAGAATCTGACAAAATTCCATTTCACCCATACTACACCATTAAAGACATTCTGGGAATCCTATTCCT
TATTTTTGTACTTATAGGTTTAGTGCTATTTACGCCAGACCTACTAGGTGACCCAGATAATTACACACCC
GCTAACCCCTTAAACACCCCACCTCACATTAAACCTGAATGATATTTTCTATTCGCCTACGCAATTCTAC
GTTCCATTCCCAACAAACTAGGAGGAGTCCTAGCCCTAGTCCTCTCCATCTTAATCCTAATCATCATTCC
ACTCCTACACACCTCAAAACAACGAAGCATAATATTTCGGCCACTTAGCCAATGTTTATTCTGATTCCTA
GTAGCAGACCTCCTCGTCCTAACATGAATTGGAGGTCAACCAGTAGAATATCCCTTCATCATCATCGGCC
AACTAGCCTCCATCTTCTACTTTATAATCCTCCTGATCCTAATACCAACAATAAATATCATCGAAAATAA
TCTGTTAAAATGAAGA