require(GeneFamilies)
options(mc.cores = getMcCores())
message("USAGE: Rscript path/2/GeneFamilies/exec/annotateFamilies.R path/2/GeneFamilies/data")
input.args <- commandArgs(trailingOnly = TRUE)
#' Compute the human readable descritions for the Gene-Families:
families.hrd <- mclapply(families.lst, annotateCluster, ipr.annos = all.ipr,
interpro.database = ipr.db)
#' Create a new data.frame extended version of 'families.df' with an extra
#' column holding the HRDs:
families.HRD.df <- families.df
families.HRD.df$description <- as.character(unlist(mclapply(families.df[, "id"],
function(fam.name) {
if (fam.name %in% names(families.hrd)) {
fam.hrd <- families.hrd[[fam.name]]
if (!is.null(fam.hrd) && !is.na(fam.hrd) && length(fam.hrd) > 0) {
fam.freq.iprs <- fam.hrd$most.frequent.IPRs
if (!is.null(fam.freq.iprs) && !is.na(fam.freq.iprs) && length(fam.freq.iprs) >
0) {
paste(unlist(lapply(fam.freq.iprs, function(x) x$SHORT.NAME)),
collapse = ",")
} else NA
} else NA
} else NA
})))
#' Save results:
save(families.hrd, families.HRD.df, file = file.path(input.args[[1]], "familyHumanReadableDescriptions.RData"))
message("DONE")
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