R/phylotaR.R

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

#' @importFrom methods is new getSlots initialize slot slotNames show
#' @importFrom stats median 
#' @importFrom utils head packageVersion read.table tail write.table
#' capture.output sessionInfo

#' @name parameters
#' @family public-pipeline
#' @title Default parameters
#' @description Returns a parameter list with default parameter values.
#' @details This function is NOT used to change the parameters in a folder.
#' Use parameters_reset() instead. The purpose of this function is to describe
#' the paramaters and present their default values.
#' @return list
#' @param wd The working directory where all output files are saved.
#' @param txid Taxonomic group of interest, allows vectors.
#' @param mkblstdb File path to makeblastdb
#' @param blstn File path to blastn
#' @param btchsz Batch size when querying NCBI
#' @param date Date when pipeline was initiated
#' @param v Print progress statements to console?
#' Statements will always be printed to log.txt.
#' @param ncps The number of threads to use in the local-alignment search tool.
#' @param mxnds The maximum number of nodes descending from a taxonomic group.
#' If there are more than this number, nodes at the lower taxonomic level are
#' analysed.
#' @param mdlthrs 'Model organism threshold'. Taxa with more sequences than this
#' number will be considered model organisms and a random mdlthrs subset of
#' their sequences will be downloaded.
#' @param mnsql The minimum length of sequence in nucleotide base pairs to
#' download.
#' @param mxsql The maximum length of sequence in nucleotide base pairs to
#' download. Any longer sequences will be ignored.
#' @param mxrtry The maximum number of attempts to make when downloading.
#' @param mxsqs The maximum number of sequences to BLAST in all-vs-all searches.
#' If there are more sequences for a node, BLAST is performed at the lower
#' taxonomic level.
#' @param mxevl The maximum E-value for a successful BLAST.
#' @param mncvrg The maximum percentile coverage defining an overlapping BLAST hit.
#' Sequences with BLAST matches with lower values are not considered orthologous.
#' @export
parameters <- function(wd='.', txid=character(), mkblstdb='', blstn='', v=FALSE,
                       ncps=1, mxnds=100000, mdlthrs=3000, mnsql=250,
                       mxsql=2000, mxrtry=100, mxsqs=50000, mxevl=1.0e-10,
                       mncvrg=51, btchsz=100, date=Sys.Date()) {
  ps <- as.list(environment())
  ps[['txid']] <- as.character(ps[['txid']])
  ps[['wt_tms']] <- c(1, 3, 6, 10, 60, 300)
  ps
}

#' @name list_ncbi_ranks
#' @family tools-public
#' @title List all NCBI Ranks
#' @description Returns a vector of all
#' NCBI taxonomic ranks in descending order.
#' @return vector
#' @export
list_ncbi_ranks <- function() {
  c("superkingdom", "kingdom", "phylum", "subphylum", "class", "superorder",
    "order", "suborder", "infraorder", "parvorder", "family", "genus",
    "species", "subspecies")
}

#' @name list_seqrec_slots
#' @family tools-public
#' @title List all SeqRec slots
#' @description Returns a vector of all available SeqRec slots of type
#' character, integer and numeric.
#' @return vector
#' @export
list_seqrec_slots <- function() {
  slt_typs <- getSlots('SeqRec')
  pull <- slt_typs %in% c('character', 'integer', 'numeric')
  names(slt_typs[pull])
}

#' @name list_clstrrec_slots
#' @family tools-public
#' @title List all ClstrRec slots
#' @description Returns a vector of all available ClstrRec slots of type
#' character, integer and numeric.
#' @return vector
#' @export
list_clstrrec_slots <- function() {
  slt_typs <- getSlots('ClstrRec')
  pull <- slt_typs %in% c('character', 'integer', 'numeric')
  names(slt_typs[pull])
}

#' @name list_taxrec_slots
#' @family tools-public
#' @title List all TaxRec slots
#' @description Returns a vector of all available TaxRec slots of type
#' character, integer and numeric.
#' @return vector
#' @export
list_taxrec_slots <- function() {
  slt_typs <- getSlots('TaxRec')
  pull <- slt_typs %in% c('character', 'integer', 'numeric')
  names(slt_typs[pull])
}