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Prefix Biostrings:: to subseq()

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hyginn 2019-11-14 22:38:53 -05:00
parent 84aa2dca0b
commit bae2d33f14
1 changed files with 6 additions and 4 deletions
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.utilities.R
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@ -2,10 +2,11 @@
# #
# Miscellaneous R code to suppport the project # Miscellaneous R code to suppport the project
# #
# Version: 1.3 # Version: 1.3.1
# Date: 2017 09 - 2017 10 # Date: 2017 09 - 2019 11
# Author: Boris Steipe # Author: Boris Steipe
# #
# V 1.3.1 prefix Biostrings:: to subseq()
# V 1.3 load msa support functions # V 1.3 load msa support functions
# V 1.2 update database utilities to support 2017 version of JSON sources # V 1.2 update database utilities to support 2017 version of JSON sources
# V 1.1 2017 updates for ABC-units # V 1.1 2017 updates for ABC-units
@ -134,7 +135,8 @@ waitTimer <- function(t, nIntervals = 50) {
fetchMSAmotif <- function(ali, mot) { fetchMSAmotif <- function(ali, mot) {
# retrieve a subset from ali that spans the sequence in mot. # Retrieve a subset from ali that spans the sequence in mot.
# Biostrings package must be installed.
# Parameters: # Parameters:
# ali MsaAAMultipleAlignment object # ali MsaAAMultipleAlignment object
# mot chr substring within ali # mot chr substring within ali
@ -169,7 +171,7 @@ fetchMSAmotif <- function(ali, mot) {
x <- as.numeric(x) x <- as.numeric(x)
x <- cumsum(x) x <- cumsum(x)
return(subseq(ali@unmasked, return(Biostrings::subseq(ali@unmasked,
start = which(x == motifStart)[1], # get the first position start = which(x == motifStart)[1], # get the first position
end = which(x == motifEnd)[1])) end = which(x == motifEnd)[1]))
} }