Pysradb to fetch SRA metadata?

[markziemann]

This looks like a more stable alternative https://github.com/saketkc/pysradb

[markziemann]

library("tictoc")
library(XML)
library(reutils)

tic()
eres <- esearch("Escherichia coli[orgn] and transcriptomic[Source] and public[Access] ", db="sra",retmax=999000)
str(uid(eres))
esum <- esummary(eres)
econtent <- content(esum, "parsed")
runvec <- econtent$Runs
runvec <- gsub("><",">><<",runvec)
runvec <- unlist(strsplit(runvec,"><"))
runs <- lapply( runvec ,function(x) { as.vector(xmlToList(x)) } )
runs <- do.call(rbind,runs)
toc()

[markziemann]

simpler

pysradb search --organism="Escherichia coli" --source="transcriptomic" --max=999000 > ecoli.tsv
awk '{print $(NF-2)}' ecoli.tsv > ecoli_runs.tsv