Remove all matched patterns in bstr sequences

Remove all matched patterns in bstr sequences

bstr_remove(bstrobj, pattern, case_sensitive = FALSE)

bstr_remove_num(bstrobj)

bstr_remove_notalpha(bstrobj)

bstr_remove_gap(bstrobj, gap_chr = "-")

Arguments

bstrobj	bstr class object or character vector
pattern	regex pattern
case_sensitive	sensitive to case in pattern (default:FALSE)
gap_chr	a gap character

Value

A bstr object.

Examples

temp <- bstr(c("ATGCCCTAG", "aTGCcCtAg"))
c(temp, remove = bstr_remove(temp, "[aT]"))
#> class: bstr,character 
#> number of sequences: 4 
#> [1]      no name 1      : ATGCCCTAG                                9 
#> [2]      no name 2      : aTGCcCtAg                                9 
#> [3]   remove.no name 1  : GCCCG                                    5 
#> [4]   remove.no name 2  : GCcCg                                    5 
c(temp, remove = bstr_remove(temp, "aT"))
#> class: bstr,character 
#> number of sequences: 4 
#> [1]      no name 1      : ATGCCCTAG                                9 
#> [2]      no name 2      : aTGCcCtAg                                9 
#> [3]   remove.no name 1  : GCCCTAG                                  7 
#> [4]   remove.no name 2  : GCcCtAg                                  7 
c(temp, remove = bstr_remove(temp, "aT", TRUE))
#> class: bstr,character 
#> number of sequences: 4 
#> [1]      no name 1      : ATGCCCTAG                                9 
#> [2]      no name 2      : aTGCcCtAg                                9 
#> [3]   remove.no name 1  : ATGCCCTAG                                9 
#> [4]   remove.no name 2  : GCcCtAg                                  7 

bstr_remove_num(bstr("ac12 -xe gg. "))
#> class: bstr,character 
#> number of sequences: 1 
#> [1]      no name 1      : ac -xe gg.                               11 
bstr_remove_notalpha(bstr("ac12 -xe gg. "))
#> class: bstr,character 
#> number of sequences: 1 
#> [1]      no name 1      : acxegg                                   6 
bstr_remove_gap(bstr("ac12 -xe gg. "))
#> class: bstr,character 
#> number of sequences: 1 
#> [1]      no name 1      : ac12 xe gg.                              12