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Update: chartr()

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hyginn 2017-10-02 14:50:33 -04:00
parent e34460cd44
commit 64dfed2daf
1 changed files with 45 additions and 16 deletions
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BIN-Sequence.R
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@ -3,12 +3,13 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-Sequence unit. # R code accompanying the BIN-Sequence unit.
# #
# Version: 1.0 # Version: 1.1
# #
# Date: 2017 09 28 # Date: 2017 09 28
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.1 Add chartr()
# 1.0 First live version 2017. # 1.0 First live version 2017.
# #
# TODO: # TODO:
@ -26,22 +27,26 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ---------------------------------------------- #TOC> ----------------------------------------------
#TOC> 1 Prepare 47 #TOC> 1 Prepare 52
#TOC> 2 Storing Sequence 61 #TOC> 2 Storing Sequence 66
#TOC> 3 String properties 90 #TOC> 3 String properties 95
#TOC> 4 Substrings 97 #TOC> 4 Substrings 102
#TOC> 5 Creating strings: sprintf() 103 #TOC> 5 Creating strings: sprintf() 108
#TOC> 6 Changing strings 134 #TOC> 6 Changing strings 139
#TOC> 6.1 stringi and stringr 162 #TOC> 6.1 stringi and stringr 191
#TOC> 6.2 dbSanitizeSequence() 172 #TOC> 6.2 dbSanitizeSequence() 201
#TOC> 7 Permuting and sampling 184 #TOC> 7 Permuting and sampling 213
#TOC> 7.1 Permutations 191 #TOC> 7.1 Permutations 220
#TOC> 7.2 Sampling 234 #TOC> 7.2 Sampling 263
#TOC> 7.2.1 Equiprobable characters 236 #TOC> 7.2.1 Equiprobable characters 265
#TOC> 7.2.2 Defined probability vector 271 #TOC> 7.2.2 Defined probability vector 300
#TOC> 8 Tasks 299 #TOC> 8 Tasks 328
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
#
#
#
#
# = 1 Prepare ============================================================= # = 1 Prepare =============================================================
@ -103,7 +108,7 @@ substr(s, 2, 4)
# = 5 Creating strings: sprintf() ========================================= # = 5 Creating strings: sprintf() =========================================
# Sprintf is a _very smart, very powerful function and has cognates in all # Sprintf is a very smart, very powerful function and has cognates in all
# other programming languages. It has a small learning curve, but it's # other programming languages. It has a small learning curve, but it's
# totally worth it: # totally worth it:
# the function takes a format string, and a list of other arguments. It returns # the function takes a format string, and a list of other arguments. It returns
@ -137,14 +142,38 @@ for (i in 99:95) {
tolower(s) tolower(s)
toupper(tolower(s)) toupper(tolower(s))
#reverse #reverse
reverse(s) reverse(s)
# chartr(old, new, x) maps all characters in x that appear in "old" to the
# correpsonding character in "new."
chartr("aeio", "uuuu", "We hold these truths to be self-evident ...")
# One could implement toupper() and tolower() with this - remember that R has
# character vectors of uppercase and lowercase letters as language constants.
chartr(paste0(letters, collapse = ""),
paste0(LETTERS, collapse = ""),
"Twinkle, twinkle little star, how I wonder what you are.")
# One amusing way to use the function is for a reversible substitution
# cypher.
set.seed(112358)
myCypher <- paste0(sample(letters), collapse = "")
lett <- paste0(letters, collapse = "")
(x <- chartr(lett, myCypher, "... seven for a secret, never to be told."))
chartr(myCypher, lett, x)
# (Nb. substitution cyphers are easy to crack!)
# substituing characters # substituing characters
(s <- gsub("IV", "i-v", s)) # gsub can change length, first argument is (s <- gsub("IV", "i-v", s)) # gsub can change length, first argument is
# a "regular expression"! # a "regular expression"!
# I use it often to delete characters I don't want ... # I use it often to delete characters I don't want ...
# ... select something, and substitute the empty string for it.
(s <- gsub("-", "", s)) (s <- gsub("-", "", s))
# For example: clean up a sequence # For example: clean up a sequence