Get records from BStringset

Source: R/blast_result_parser.R

an object of class BStringset stores sequences and headers from FASTA or FASTQ files. See Biostrings::readBStringSet(). This function helps users to filter sequences by headers with full or partial match.

subset_bstringset(x, y, partial_match = TRUE)

Arguments

x

character vector of query ids
y

an object of class BStringset from which sequences to be filtered
partial_match

logical (default TRUE).

  1. TRUE : return sequences if element of x matches anywhere in the headers of y.

  2. FALSE : return sequences only of exact match occur between element of x and headers of y.

Value

an object of class BStringset

Examples

if (FALSE) {
x <- c("EIT75269.1",
  "TGO19408.1",
  "KAF2153260.1",
  "OAA41719.1",
  "OSS52177.1",
  "XP_018252424.1",
  "XP_008598593.1",
  "KXN65110.1",
  "XP_018147989.1",
  "XP_022493698.1",
  "RII05464.1",
  "XP_018703519.1",
  "RZR67285.1",
  "OLY78428.1",
  "XP_007819064.1",
  "PQK17331.1",
  "KXN66278.1",
  "CRK21695.1",
  "CVK85925.1",
  "KID81639.1")
y_file <- system.file("extdata" ,"blast_output_01.fasta" , package = "phyloR")
y <- Biostrings::readBStringSet(y_file)
## subset fasta by partial match
sub <- phyloR::subset_bstringset(x = x , y = y ,partial_match = T)
subset_bstringset(x , y,  partial_match  = TRUE)
}