demos/demo_run.R

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

# Example: Rscript demos/demo_run.R /workspaces/blast/bin/

# LIBS
#library(phylotaR)
devtools::load_all()

# VARS ----
demos <- c(
  "anisoptera" = "6962", "acipenseridae" = "7900",
  "tinamiformes" = "8802", "aotus" = "9504",
  "bromeliaceae" = "4613", "cycadidae" = "1445963",
  "eutardigrada" = "42242", "kazachstania" = "71245",
  "platyrrhini" = "9479", "primates" = "9443"
)
demos <- demos[1:9]
# set these paths for your own system
args <- commandArgs(trailingOnly = TRUE)
if (length(args) < 1) {
  print("Please provide a NCBI blast path")
  quit(status = -1)
} else {
  message("Only the first path will be used.")
  ncbi_dr <- args[1]
}

# FOR LOOP ----
for (i in seq_along(demos)) {
  txid <- demos[[i]]
  wd <- file.path(getwd(), "demos", names(demos)[[i]])
  # create folder, delete if already exists
  if (file.exists(wd)) {
    unlink(wd, recursive = TRUE)
  }
  dir.create(wd)
  # run
  phylotaR::setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr, v = TRUE)
  run(wd = wd)
}

# TIMINGS ----
timings <- vector(mode = "list", length = length(demos))
names(timings) <- names(demos)
for (i in seq_along(demos)) {
  wd <- file.path(getwd(), "demos", names(demos)[[i]])
  timings[[i]] <- get_stage_times(wd)
}

# CLSQ STATS ----
clsq <- vector(mode = "list", length = length(demos))
names(clsq) <- names(demos)
for (i in seq_along(demos)) {
  wd <- file.path(getwd(), "demos", names(demos)[[i]])
  phylota <- read_phylota(wd)
  clsq[[i]] <- c(
    "Taxa" = length(phylota@txids),
    "Sequences" = length(phylota@sids),
    "Clusters" = length(phylota@cids)
  )
}

# MARKDOWN ----
mrkdwn <- "Taxon|N. taxa|N. sequences|N. clusters|Taxise (mins.)|"
mrkdwn <- paste0(mrkdwn, "Download (mins.)|Cluster (mins.)|Cluster2 (mins.)|")
mrkdwn <- paste0(mrkdwn, "Total (mins.)|\n")
mrkdwn <- paste0(mrkdwn, "|:--|--:|--:|--:|--:|--:|--:|--:|--:|\n")
for (i in seq_along(timings)) {
  mrkdwn <- paste0(
    mrkdwn, Hmisc::capitalize(names(timings)[[i]]), "|",
    clsq[[i]][["Taxa"]], "|", clsq[[i]][["Sequences"]], "|",
    clsq[[i]][["Clusters"]], "|",
    signif(timings[[i]][["taxise"]], 2), "|",
    signif(timings[[i]][["download"]], 2), "|",
    signif(timings[[i]][["cluster"]], 2), "|",
    signif(timings[[i]][["cluster\\^2"]], 2), "|",
    signif(sum(timings[[i]]), 2), "|\n"
  )
}
cat(mrkdwn)