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