create_cobalt_options: Create the COBALT options
In richelbilderbeek/cobaltr: Interface Io COBALT

create_cobalt_options

R Documentation

Create the COBALT options

Description

Create the COBALT options

Usage

create_cobalt_options(
  search_pattern_filename = file.path(get_default_cobalt_folder(), "patterns"),
  domain_database_filename = file.path(get_default_cobalt_folder(), "cdd"),
  conserved_block_filename = file.path(get_default_cobalt_folder(), "cdd.blocks"),
  residue_frequencies_filename = file.path(get_default_cobalt_folder(), "cdd.freq"),
  destination_filename = "",
  pac_filename = "",
  conserved_domain_threshold = 0.01,
  filler_threshold = 0.01,
  terminal_open_gap_penalty = 5,
  terminal_extend_gap_penalty = 1,
  open_gap_in_middle_penalty = 11,
  middle_extend_gap_penalty = 1,
  conservation_score_threshold = 0.67,
  dfb_added_weight = 0.5,
  ffb_added_weight = 1,
  no_rps = FALSE,
  search_around_ccs = TRUE,
  score_matrix_name = "BLOSUM62",
  pseudocount_constant = 2,
  use_fastme = FALSE,
  do_dry_run = FALSE,
  verbose = FALSE
)

Arguments

`search_pattern_filename`	filename containing search patterns, the COBALT `-p` option
`domain_database_filename`	domain database filename, the COBALT `-db` option
`conserved_block_filename`	filename containing conserved blocks, the COBALT `-b` option
`residue_frequencies_filename`	filename containing residue frequencies, the COBALT `-f` option
`destination_filename`	filename for destination text seqalign the COBALT `-seqalign` option
`pac_filename`	name of the file containing pairwise alignment constraints, one per line, each of the following form: `seq1_idx seq1_start seq1_end seq2_idx seq2_start seq2_end`. The COBALT `-c` flag
`conserved_domain_threshold`	the threshold of the E-value for selecting conserved domains. The COBALT `-evalue` flag
`filler_threshold`	the threshold of the E-value for aligning filler segments. The COBALT `-evalue2` flag
`terminal_open_gap_penalty`	the gap open penalty for initial/terminal gaps. The COBALT `-g0` flag
`terminal_extend_gap_penalty`	The COBALT `-e0` flag
`open_gap_in_middle_penalty`	The COBALT `-g1` flag
`middle_extend_gap_penalty`	The COBALT `-e1` flag
`conservation_score_threshold`	the minimum average score needed for a multiple alignment column to be considered as conserved. The COBALT `-ccc` flag
`dfb_added_weight`	the amount of extra weight (0..1) to give the actual sequence letter at that position, The COBALT `-dfb` flag
`ffb_added_weight`	the amount of extra weight (0..1) to give the actual sequence letter at that position when assigning filler residue frequencies. The COBALT `-ffb` flag
`no_rps`	do not perform initial RPS blast search The COBALT `-norps` flag
`search_around_ccs`	look for conserved columns and iterate if any are found. The COBALT `-iter` flag
`score_matrix_name`	name of the COBALT score matrix. Use get_matrix_names to get a list of all possible matrix names
`pseudocount_constant`	the pseudocount constant The COBALT `-pseudo` flag
`use_fastme`	use FastME tree generation algorithm (instead of neighbor joining). The COBALT `-fastme` flag
`do_dry_run`	Do a dry run, that is, only test all preconditions The COBALT `-dryrun` flag
`verbose`	verbose output the COBALT `-v` option