nc (version 2019.9.16)

capture_all_str: Capture all matches in a single subject string

Description

Extract each match of a regex pattern from one subject string. It is for the common case of extracting all matches of a regex from a single multi-line text file subject. This function uses var_args_list to analyze the arguments.

Usage

capture_all_str(subject.vec, ..., engine = getOption("nc.engine", 
    "PCRE"), collapse = "\n")

Arguments

subject.vec

The subject character vector. We use paste to collapse subject.vec (by default using newline) and treat it as single character string to search.

…

name1=pattern1, fun1, etc, which creates the regex (pattern1), uses fun1 for conversion, and creates column name1 in the output. These arguments specify the regular expression pattern and must be character/function/list. All patterns must be character vectors of length 1. If the pattern is a named argument in R, it becomes a capture group in the regex. All patterns are pasted together to obtain the final pattern used for matching. Each named pattern may be followed by at most one function which is used to convert the previous named pattern. Lists are parsed recursively for convenience.

engine

character string, one of PCRE, ICU, RE2

collapse

string used with paste to collapse subject.vec

Value

data.table with one row for each match, and one column for each capture group.

Examples

# NOT RUN {
chr.pos.vec <- c(
  "chr10:213,054,000-213,055,000",
  "chrM:111,000-222,000",
  "this will not match",
  NA, # neither will this.
  "chr1:110-111 chr2:220-222") # two possible matches.
keep.digits <- function(x)as.integer(gsub("[^0-9]", "", x))
## By default elements of subject are treated as separate lines (and
## NAs are removed). Named arguments are used to create capture
## groups, and conversion functions such as keep.digits are used to
## convert the previously named group.
int.pattern <- list("[0-9,]+", keep.digits)
(match.dt <- nc::capture_all_str(
  chr.pos.vec,
  chrom="chr.*?",
  ":",
  chromStart=int.pattern,
  "-",
  chromEnd=int.pattern))
str(match.dt)

## use engine="ICU" for unicode character classes
## http://userguide.icu-project.org/strings/regexp e.g. match any
## character with a numeric value of 2 (including japanese etc).
nc::capture_all_str(
  "\u4e8c \u4e09 2 3 ",
  two="[\\p{numeric_value=2}]",
  engine="ICU")

## Extract all fields from each alignment block, using two regex
## patterns, then dcast.
library(data.table)
info.txt.gz <- system.file(
"extdata", "SweeD_Info.txt.gz", package="nc")
info.vec <- readLines(info.txt.gz)
info.vec[24:40]
info.dt <- nc::capture_all_str(
  sub("Alignment ", "//", info.vec),
  "//",
  alignment="[0-9]+",
  fields="[^/]+")
(fields.dt <- info.dt[, nc::capture_all_str(
  fields,
  "\t+",
  variable="[^:]+",
  ":\t*",
  value=".*"),
  by=alignment])
(fields.wide <- dcast(fields.dt, alignment ~ variable))

## Capture all csv tables in report.
report.txt.gz <- system.file(
  "extdata", "SweeD_Report.txt.gz", package="nc")
report.vec <- readLines(report.txt.gz)
(report.dt <- nc::capture_all_str(
  report.vec,
  "//",
  alignment="[0-9]+",
  "\n",
  csv="[^/]+"
)[, {
  fread(text=csv)
}, by=alignment])

## Join report with info fields.
report.dt[fields.wide, on=.(alignment)]

# }