field: Capture a field

In nc: Named Capture to Data Tables

Capture a field

Description

Capture a field with a pattern of the form list("field.name", between.pattern, field.name=list(...)) – see examples.

Usage

field(field.name, between.pattern, 
    ...)

Arguments

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.

Value

Pattern list which can be used in capture_first_vec, capture_first_df, or capture_all_str.

Author(s)

Toby Dylan Hocking

Examples

## Two ways to create the same pattern.
str(list("Alignment ", Alignment="[0-9]+"))
## To avoid typing Alignment twice use:
str(nc::field("Alignment", " ", "[0-9]+"))

## An example with lots of different fields.
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))

nc documentation built on Sept. 1, 2023, 1:07 a.m.