sub_all: Extract and replace all subsequences from a bstr sequences

In t-arae/bstringr: A package to use a character vector as a biological strings

Description

Extract and replace all subsequences from a bstr sequences

Usage

bstr_sub_all(bstrobj, from = list(1L), to = list(-1L), length)

bstr_sub_all(bstrobj, from = list(1L), to = list(-1L), length, omit_na = FALSE) <- value

bstr_sub_replace_all(..., replacement, value = replacement)

bstr_sub_all_replace(..., replacement, value = replacement)

Arguments

bstrobj	bstr class object or character vector
from	a list of integer vectors giving the start indexes or a list of two-column matrices, each of type cbind(from, to)
to	a list of integer vectors giving the end indexes
length	a list of integer vectors giving the substring lengths
omit_na	a single logical value; indicates whether missing values in any of the indexes or in value leave the part of the corresponding input string unchanged [replacement function only]
value	a list of character vectors defining the replacement strings [replacement function only]
...	arguments to be passed to bstr_sub_all<-
replacement	alias of value [wherever applicable]

Examples

(temp <- dstr_rand_seq(3, 20, "[AT]", seed = 1))

(pos_A_trails <- stringr::str_locate_all(temp, "A{2,}"))

# Extract all A trails
bstr_sub_all(temp, pos_A_trails)

# Substitute all A trails by x
bstr_sub_all(temp, pos_A_trails) <- "x"
temp

# Substitute all A trails by case switched ones
original <- change <- dstr_rand_seq(2, 10, "[AaT]", seed = 1)
pos_A_trails <- stringr::str_locate_all(change, "[Aa]{2,}")
switched_A_trails <-
  bstr_sub_all(change, pos_A_trails) %>%
  lapply(bstr_switch_case)
bstr_sub_all(change, pos_A_trails) <- switched_A_trails
c(original[1], change[1], original[2], change[2])

t-arae/bstringr documentation built on March 18, 2021, 3:08 a.m.