metadata_find&fetch.R

library(ORFik)
library(data.table)
library(dplyr)

bioprojects <- ORFik::get_bioproject_candidates("(Ribosomal footprinting) OR (Ribosome footprinting) OR (Ribosome profiling) OR ribo-seq",add_study_title = TRUE)
processed_records <- system("ls SraRunInfo/", intern = TRUE) %>% sub("SraRunInfo_","",.) %>% sub(".csv","",.)
unprocessed <- bioprojects$id[!(bioprojects$id %in% processed_records)]
bioprojects$abstract <- ""

writeSRA <- function(candidate) {
  print(candidate)
  sra <- try(download.SRA.metadata(candidate, outdir = "SraRunInfo", rich.format = TRUE))
  return(candidate)
}


rna_seq_meta <- lapply(unprocessed, function(x) writeSRA(x))

abstracts <- system("ls SraRunInfo/abstract_*", intern = TRUE)

abstracts <- sapply(abstracts, function(x) gsub("\"","",readLines(x)[[2]]), USE.NAMES = TRUE)

names(abstracts) <- names(abstracts)  %>% sub(".*abstract_","",.) %>% sub(".csv","",.)
bioprojects[match(names(abstracts),id), abstract := abstracts]

fwrite(bioprojects, "bioprojects.csv")