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rewrite getMYSPE()

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hyginn 2021-09-18 12:00:51 -04:00
parent 9143b784e9
commit 86d619ad51
1 changed files with 37 additions and 31 deletions
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68
.utilities.R
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@ -2,10 +2,11 @@
# #
# Miscellaneous R code to support the project # Miscellaneous R code to support the project
# #
# Version: 1.4 # Version: 1.5
# Date: 2017-09 - 2020-09 # Date: 2017-09 - 2021-09
# Author: Boris Steipe # Author: Boris Steipe
# #
# V 1.5 rewrite getMYSPE()
# V 1.4 Maintenance, and new validation utilities # V 1.4 Maintenance, and new validation utilities
# V 1.3.1 prefix Biostrings:: to subseq() # V 1.3.1 prefix Biostrings:: to subseq()
# V 1.3 load msa support functions # V 1.3 load msa support functions
@ -20,32 +21,32 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ----------------------------------------------------------- #TOC> -----------------------------------------------------------
#TOC> 1 SCRIPTS TO SOURCE 52 #TOC> 1 SCRIPTS TO SOURCE 53
#TOC> 2 PACKAGES 58 #TOC> 2 PACKAGES 59
#TOC> 3 DATA & CONSTANTS 69 #TOC> 3 DATA & CONSTANTS 70
#TOC> 4 SUPPORT FUNCTIONS 116 #TOC> 4 SUPPORT FUNCTIONS 117
#TOC> 4.01 objectInfo() 119 #TOC> 4.01 objectInfo() 120
#TOC> 4.02 biCode() 147 #TOC> 4.02 biCode() 148
#TOC> 4.03 sameSpecies() 181 #TOC> 4.03 sameSpecies() 182
#TOC> 4.04 validateFA() 201 #TOC> 4.04 validateFA() 202
#TOC> 4.05 readFASTA() 309 #TOC> 4.05 readFASTA() 310
#TOC> 4.06 writeFASTA() 344 #TOC> 4.06 writeFASTA() 345
#TOC> 4.07 pBar() 377 #TOC> 4.07 pBar() 378
#TOC> 4.08 waitTimer() 399 #TOC> 4.08 waitTimer() 400
#TOC> 4.09 fetchMSAmotif() 427 #TOC> 4.09 fetchMSAmotif() 428
#TOC> 4.10 H() (Shannon entropy) 471 #TOC> 4.10 H() (Shannon entropy) 472
#TOC> 4.11 CX() (ChimeraX remote command) 484 #TOC> 4.11 CX() (ChimeraX remote command) 485
#TOC> 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS 541 #TOC> 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS 542
#TOC> 5.01 seal() 543 #TOC> 5.01 seal() 544
#TOC> 5.02 getMYSPE() 547 #TOC> 5.02 getMYSPE() 548
#TOC> 5.03 selectPDBrep() 558 #TOC> 5.03 selectPDBrep() 564
#TOC> 5.04 sealKey() 593 #TOC> 5.04 sealKey() 599
#TOC> 5.05 selectChi2() 623 #TOC> 5.05 selectChi2() 629
#TOC> 5.06 selectENSP() 636 #TOC> 5.06 selectENSP() 642
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -545,12 +546,17 @@ seal <- function(x.1L) { .Call(digest:::digest_impl,x.1L,3L,-1L,-0,-0,-0) }
# == 5.02 getMYSPE() ======================================================= # == 5.02 getMYSPE() =======================================================
# DEV: x <- 1003141593
getMYSPE <- function(x) { getMYSPE <- function(x) {
dat <- readRDS("./data/sDat.rds") dat <- readRDS("./data/MYSPEdat.rds")
map <- readRDS("./data/MYSPEmap.rds") key <- digest::digest(as.character(x), algo = "md5")
key <- gsub(".+(....).$","\\1", x) if (length(grep(key, rownames(dat))) != 1) {
x <- dat$species[map[key,"iMYSPE"]] stop(paste("This student number is not recognized.",
names(x) <- dat$taxID[map[key,"iMYSPE"]] "If this is not a typo, please contact your instructor."))
}
x <- dat[key, "species"]
names(x) <- dat[key, "taxID"]
return(x) return(x)
} }