R/field.R

field <- structure(function # Capture a field
### Capture a field with a pattern of the form
### list("field.name", between.pattern,
### field.name=list(...)) -- see examples.
(field.name,
### Field name, used as a pattern and as a capture group (output
### column) name.
  between.pattern,
### Pattern to match after field.name but before the field value.
  ...
### Pattern(s) for matching field value.
){
  if(!(is.character(field.name) && length(field.name)==1))stop(
    "first argument of field must be character string (field name)")
  list(
    field.name,
    between.pattern,
    group(field.name, ...))
### Pattern list which can be used in capture_first_vec,
### capture_first_df, or capture_all_str.
}, ex=function(){

  info.txt.gz <- system.file(
    "extdata", "SweeD_Info.txt.gz", package="nc")
  info.vec <- readLines(info.txt.gz)
  info.vec[24:40]
  ## For each Alignment there are many fields which have a similar
  ## pattern, and occur in the same order. One way to capture these
  ## fields is by coding a pattern that says to look for all of those
  ## fields in that order. Each field is coded using this helper
  ## function.
  g <- function(name, fun=identity, suffix=list()){
    list(
      "\t+",
      nc::field(name, ":\t+", ".*"),
      fun,
      suffix,
      "\n+")
  }
  nc::capture_all_str(
    info.vec,
    nc::field("Alignment", " ", "[0-9]+"),
    "\n+",
    g("Chromosome"),
    g("Sequences", as.integer),
    g("Sites", as.integer),
    g("Discarded sites", as.integer),
    g("Processing", as.integer, " seconds"),
    g("Position", as.integer),
    g("Likelihood", as.numeric),
    g("Alpha", as.numeric))

  ## Another example where field is useful.
  trackDb.txt.gz <- system.file(
    "extdata", "trackDb.txt.gz", package="nc")
  trackDb.vec <- readLines(trackDb.txt.gz)
  cat(trackDb.vec[101:115], sep="\n")
  int.pattern <- list("[0-9]+", as.integer)
   cell.sample.type <- list(
    cellType="[^ ]*?",
    "_",
    sampleName=list(
      "McGill",
      sampleID=int.pattern),
    dataType="Coverage|Peaks")
  ## Each block in the trackDb file begins with track, followed by a
  ## space, followed by the track name. That pattern is coded below,
  ## using field:
  track.pattern <- nc::field(
    "track",
    " ",
    cell.sample.type,
    "|",
    "[^\n]+")
  nc::capture_all_str(trackDb.vec, track.pattern)

  ## Each line in a block has the same structure (field name, space,
  ## field value). Below we use the field function to extract the
  ## color line, along with columns for each of the three channels
  ## (red, green, blue).
  any.lines.pattern <- "(?:\n[^\n]+)*"
  nc::capture_all_str(
    trackDb.vec,
    track.pattern,
    any.lines.pattern,
    "\\s+",
    nc::field(
      "color", " ",
      red=int.pattern, ",",
      green=int.pattern, ",",
      blue=int.pattern))

})

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nc documentation built on March 25, 2020, 5:10 p.m.