Question

Download Fasta in R

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3.5 years ago

Kenan.gk ▴ 10

How to download human fasta format in R programming?

FASTA R • 1.1k views

ADD COMMENT • link updated 2.5 years ago by Ram 45k • written 3.5 years ago by Kenan.gk ▴ 10

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That's out of context. You mean a specific file or what? Check Biostrings::readDNAStringSet().

ADD REPLY • link 3.5 years ago by ATpoint 89k

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thank you so much :)

ADD REPLY • link 3.5 years ago by Kenan.gk ▴ 10

score 1 · Answer 1 · 2022-03-13

I am turning ATpoint's comment into an answer, hope that is ok.

 library(Biostrings)      
 readDNAStringSet("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz")

Most R functions that can read in data can use URL connections in the same ways as local files, and also deal with compressed files.