Question: Download NCBI genome sequences from Python
0
gravatar for jolespin
2.4 years ago by
jolespin120
United States
jolespin120 wrote:

I have data that looks like:

1. Cronobacter phage Dev2
Characterization of lytic Cronobacter turicensis phage Dev2 isolated from wastewater treatment
Kingdom: Viruses
Chromosome: 1
Genome ID: 36224

2. Pseudomonas phage vB_Pae-TbilisiM32
Modified complete genome sequence of Pseudomonas phage vB_Pae-TbilisiM32
Kingdom: Viruses
Chromosome: 1
Genome ID: 13968

How can I fetch the genome sequences from these in Python? I know how to do it for specific kegg genes using bioservices but how do I get full genomes?

ADD COMMENTlink modified 2.4 years ago by Jenez520 • written 2.4 years ago by jolespin120
1
gravatar for Jenez
2.4 years ago by
Jenez520
Sweden
Jenez520 wrote:

Biopython has this functionality.

http://biopython.org/DIST/docs/tutorial/Tutorial.html

See section '9.6 EFetch: Downloading full records from Entrez'

ADD COMMENTlink written 2.4 years ago by Jenez520
0
gravatar for bioExplorer
2.4 years ago by
bioExplorer3.7k
bioExplorer3.7k wrote:

Do you have the corresponding accessions? Or can you get them?

If yes, I have a Python script which uses the accessions and downloads the sequences.

Looking forward to your response. :)

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by bioExplorer3.7k
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