Download NCBI genome sequences from Python
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?
2 answers
Biopython has this functionality.
http://biopython.org/DIST/docs/tutorial/Tutorial.html
See section '9.6 EFetch: Downloading full records from Entrez'
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. :)
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lakhujanivijay
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