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jashapiro/get_ena_ftp.R

Last active June 30, 2020 12:52
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An R function to get a table of ENA FTP urls for an SRA project
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get_ena_ftp.R
get_ena_ftp <- function(SRA_project){
ena_url <- stringr::str_interp("http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=${SRA_project}&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes")
ena_table <- readr::read_tsv(ena_url) %>%
tidyr::separate_rows(fastq_ftp, fastq_md5, fastq_bytes, sep = ";")
}
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