itsx: Extract Ribosomal RNA Gene Regions from Eukaryotic DNA

In brendanf/rITSx: Extract ITS and Neighboring Regions from Eukaryotic DNA Sequences

Description

Calls the external program ITSx, which must be installed and on the path. For more information on installation, algorithms, or options, see http://microbiology.se/software/itsx/.

Usage

itsx(
  in_file,
  out_root = tempfile("itsx"),
  taxon = "fungi",
  e_value = 1e-05,
  s_value = 0,
  n_value = 2,
  selection_priority = c("score", "sum", "domains", "eval"),
  search_eval = 0.01,
  search_score = NULL,
  allow_single_domain = c(1e-09, 0),
  allow_reorder = FALSE,
  complement = TRUE,
  cpu = 1,
  multi_thread = cpu > 1,
  heuristics = FALSE,
  nhmmer = FALSE,
  summary = TRUE,
  graphical = TRUE,
  fasta = TRUE,
  preserve = FALSE,
  save_regions = c("ITS1", "ITS2"),
  anchor = 0,
  require_anchor = 0,
  only_full = FALSE,
  partial = 0,
  concat = FALSE,
  minlen = 0,
  positions = TRUE,
  table = FALSE,
  detailed_results = FALSE,
  not_found = TRUE,
  truncate = TRUE,
  silent = FALSE,
  graph_scale = 0,
  save_raw = FALSE,
  read_function = NULL
)

Arguments

in_file	Name of a fasta file to read sequences from. Alternatively, a member of classes ShortRead, DNAStringSet or SeqFastadna, in which case the sequences will be written to a temporary .fasta file.
out_root	Root name for all output files. The default will put these in a pseudorandomly generated file name in the R temp directory, which is probably not what you want if you intend to access them later.
taxon	The taxonomic group(s) to attempt to find rDNA from. See the manual for ITSx for available options. In contrast to the default for ITSx ("all") the default for this function is "fungi".
e_value	E-value cutoff for inclusion in results.
s_value	Score cutoff for inclusion in results.
n_value	Number of domains required for inclusion in results.
selection_priority	Priority for determining sequence origin.
search_eval	Actual E-value cutoff for HMMER search. Only one of search_eval and search_score may be supplied.
search_score	Actual score cutoff for HMMER search. Only one of search_eval and search_score may be supplied.
allow_single_domain	Allow inclusion of sequences where only one domain match is found. Either FALSE or a (double, integer) pair giving inclusion criteria for e_value and Score.
allow_reorder	Allow inclusion of sequences where the domains do not occur in the expected order.
complement	Search the reverse complement of each sequence also.
cpu	Number of threads to use.
multi_thread	Whether to use multiple threads or not.
heuristics	Use heuristic filtering to speed up HMMER search.
nhmmer	Use nhmmer instead of hmmsearch.
summary	Output summary results in [out_root].summary.txt.
graphical	Output graphical results in [out_root].graph.
fasta	Output full ITS (ITS1 + 5.8S + ITS2) results in [out_root].full.fasta.
preserve	Use original sequence headers instead of writing new ones.
save_regions	Additional reagions to save output for; Options are one or more of "SSU", "ITS1", "5.8S", "ITS2", "LSU", or "all" or "none". There will be output in [out_root].SSU.fasta, [out_root].ITS1.fasta, etc.
anchor	Number of extra bases included at the beginning and end of each region. Only one of anchor and require_anchor may be given.
require_anchor	As anchor, but the anchor bases are required to be present for the region to be included in output. Only one of anchor and require_anchor may be given.
only_full	Limit output to full length ITS1 and ITS2 regions.
partial	Save additional files for partial regions. The argument give the minimum number of bases required. These will be saved as [out_root].full_and_partial.fasta for the full ITS region, and as [out_root].SSU.full_and_partial.fasta, [out_root].ITS1.full_and_partial.fasta, etc. for the other regions.
concat	Output concatenated ITS1 and ITS2 regions in [out_root].concat.fasta.
minlen	Minimum length for ITS regions to be included in concat.
positions	Output a table of positions where HMMER matches were detected in [out_root].positions.txt.
table	Output a table of ITS results in [out_root].hmmer.table.
detailed_results	Output detailed results in [out_root].extraction.results.
not_found	Output a list of sequences for which no match was found in [out_root]_no_detections.txt.
truncate	Remove ends of ITS sequences if they extend beyond the ITS region.
silent	Supress printing of information to screen.
graph_scale	Sets the scale of the graphical output.
save_raw	Save raw data from searches in directory [out_root]_ITSx_raw_output.
read_function	A function which can be used to read a fasta format file, such as ShortRead::readFasta, Biostrings::readDNAStringSet, or seqinr::read.fasta. If a value is given, then all output files will be read and then deleted, using the given function to read fasta files. If no fasta output is requested, then this behavior can be triggered by giving any other value, for example TRUE (but also FALSE!)

Details

For basic usage, this function only checks the arguments and gernerates the function call. However, to simplify integration with R-based workflows, it is also possible to specify the in_file as one of several R classes that hold DNA sequences , and by specifying a read_function, the output file(s) can be automatically read into R and returned as members of a list.

Value

The return value of the ITSx program, or if read_function is given, a list containing the contents of all files which were created (except the raw output).

brendanf/rITSx documentation built on April 6, 2020, 4:37 p.m.