# SPEED TEST DOWNLOAD STAGE WITH AND WITHOUT RESTEZ
# LIBS ----
devtools::load_all('~/Coding/restez')
devtools::load_all('~/Coding/phylotaR')
# VARS ----
wd <- 'beavers'
restez_path <- '~/Desktop/beavers_restez'
txid <- 1963757
ncbi_dr <- '/usr/bin'
# RUN PHYLOTAR ----
if (dir.exists(wd)) {
unlink(x = wd, recursive = TRUE)
}
dir.create(wd)
phylotaR::setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr, v = TRUE, btchsz = 100)
taxise_run(wd = wd)
# SPEED TEST 1
without_restez <- system.time(expr = {
download_run(wd = wd)
})
# user system elapsed
# 121.104 32.604 467.001
# user system elapsed
# 63.128 0.883 438.626
# SET-UP RESTEZ ----
restez_path_set(filepath = restez_path)
db_download(preselection = '15') # select 15 for rodents
restez_connect()
db_create()
restez_disconnect()
restez_status()
# RESET PHYLOTAR ----
reset(wd = wd, stage = 'download', hard = TRUE)
# SPEED TEST 2
restez_path_set(filepath = restez_path)
restez_connect()
with_restez <- system.time(expr = {
download_run(wd = wd)
})
restez_disconnect()
# user system elapsed
# 71.983 14.783 234.640
# TAKE HOME STAT
# twice as faster
pfaster <- signif((467.001/234.640), 3)
cat(pfaster, 'x faster with restez\n', sep = '')
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