Declare the token grammar of an export file name

A cr_filename_grammar states how one export file name decomposes into design facts: which trailing token is the replicate index, which leading labels are stripped, which substrings are tokens, and which whole-name shapes are legal at all.

Usage

cr_filename_grammar(
  tokens = list(),
  defaults = list(),
  core_patterns = character(),
  typo_fixes = character(),
  prefix_strip = character(),
  replicate = "[0-9]+(?:\\.[0-9]+)?",
  sep = "_",
  normalise_space = TRUE
)

# S3 method for class 'cr_filename_grammar'
print(x, ...)

Arguments

tokens

Named list (or named character vector) of regular expressions. Each is searched for in the name core; the matched text becomes the value of a column named after the list element.

defaults

Named list of values to use when a token is absent. Elements with no entry default to NA.

core_patterns

Character vector of regular expressions. The core (the name with extension, markers, replicate index and prefix removed) must match at least one of them. Empty means no whitelist.

typo_fixes

Named character vector of pattern = replacement repairs applied before anything else is parsed.

prefix_strip

Character vector of leading labels to strip from the core, longest first.

replicate

Regular expression for the trailing replicate token. Default "[0-9]+(?:\\.[0-9]+)?", which accepts both 1 and 1.1.

sep

Token separator. Default "_".

normalise_space

Logical. Convert runs of whitespace to sep and collapse repeated separators. Default TRUE.

x

A cr_filename_grammar.

...

Ignored.

Value

An object of class cr_filename_grammar (a list).

x, invisibly.

Details

The core_patterns whitelist exists because the absence of a token is itself meaningful — a name with no interval token is the untreated reference arm, a name with no concentration token is a vehicle control. A mistyped token therefore matches nothing, falls through to the defaults, and silently reclassifies a treated unit as a vehicle control, pulling it into the control denominator of its own batch. With a whitelist in place such a name is a hard error instead.

prefix_strip entries are removed longest-first, so a short label cannot consume a longer one that starts with the same characters.

See also

cr_parse_paths(), cr_path_spec().

Other import: cr_assign_units(), cr_centroid_overlap(), cr_column_map(), cr_extract_markers(), cr_marker_rules(), cr_merge_rules(), cr_parse_paths(), cr_path_spec(), cr_read_cellprofiler(), cr_read_cells(), cr_read_design(), cr_read_export(), cr_read_exports(), cr_read_qupath(), cr_read_segmantr(), cr_unit_map()

Examples

g <- cr_filename_grammar(
  tokens = list(interval = "[0-9]+min", dose = "[0-9]+uM",
                mode = "treated|vehicle"),
  defaults = list(interval = "none", dose = "vehicle"),
  core_patterns = c("^vehicle$",
                    "^[0-9]+min_vehicle$",
                    "^[0-9]+uM_treated$",
                    "^[0-9]+min_[0-9]+uM_treated$"),
  prefix_strip = c("CompoundA", "CompoundB")
)
g
#> <cr_filename_grammar>
#> • tokens: interval, dose, and mode
#> • core patterns: 4
#> • prefixes stripped: 2
#> • replicate: "[0-9]+(?:\\.[0-9]+)?"