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add digest:: and jsonlite::, and sameSpecies(),

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hyginn 2020-09-21 21:34:45 +10:00
parent b1d712891f
commit cfbfee9dba
1 changed files with 59 additions and 28 deletions
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.utilities.R
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@ -6,7 +6,7 @@
# Date: 2017-09 - 2020-09 # Date: 2017-09 - 2020-09
# Author: Boris Steipe # Author: Boris Steipe
# #
# V 1.4 Maintenance # 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
# 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
@ -23,19 +23,21 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ----------------------------------------------------------- #TOC> -----------------------------------------------------------
#TOC> 1 SCRIPTS TO SOURCE 42 #TOC> 1 SCRIPTS TO SOURCE 45
#TOC> 2 SUPPORT FUNCTIONS 49 #TOC> 2 PACKAGES 51
#TOC> 2.1 objectInfo() 52 #TOC> 3 SUPPORT FUNCTIONS 62
#TOC> 2.2 biCode() 80 #TOC> 3.1 objectInfo() 65
#TOC> 2.3 pBar() 114 #TOC> 3.2 biCode() 93
#TOC> 2.4 waitTimer() 136 #TOC> 3.3 sameSpecies() 127
#TOC> 2.5 fetchMSAmotif() 164 #TOC> 3.4 pBar() 146
#TOC> 2.6 H() (Shannon entropy) 208 #TOC> 3.5 waitTimer() 168
#TOC> 3 DATA 222 #TOC> 3.6 fetchMSAmotif() 196
#TOC> 3.1 REFspecies 224 #TOC> 3.7 H() (Shannon entropy) 240
#TOC> 4 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS 239 #TOC> 4 DATA 254
#TOC> 4.1 getMYSPE() 242 #TOC> 4.1 REFspecies 256
#TOC> 4.2 selectPDBrep() 251 #TOC> 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS 271
#TOC> 5.1 getMYSPE() 274
#TOC> 5.2 selectPDBrep() 283
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -46,11 +48,21 @@ source("./scripts/ABC-dbUtilities.R")
source("./scripts/ABC-writeALN.R") source("./scripts/ABC-writeALN.R")
source("./scripts/ABC-writeMFA.R") source("./scripts/ABC-writeMFA.R")
# = 2 PACKAGES ============================================================
# = 2 SUPPORT FUNCTIONS =================================================== if (! requireNamespace("digest", quietly = TRUE)) {
install.packages("digest")
}
if (! requireNamespace("jsonlite", quietly = TRUE)) {
install.packages("jsonlite")
}
# == 2.1 objectInfo() ====================================================== # = 3 SUPPORT FUNCTIONS ===================================================
# == 3.1 objectInfo() ======================================================
objectInfo <- function(x) { objectInfo <- function(x) {
# Function to combine various information items about R objects # Function to combine various information items about R objects
# #
@ -78,7 +90,7 @@ objectInfo <- function(x) {
} }
# == 2.2 biCode() ========================================================== # == 3.2 biCode() ==========================================================
biCode <- function(s) { biCode <- function(s) {
# Make a 5 character "biCode" from a binomial name by concatening # Make a 5 character "biCode" from a binomial name by concatening
# the uppercased first three letter of the first word and the first # the uppercased first three letter of the first word and the first
@ -112,8 +124,27 @@ biCode <- function(s) {
} }
# == 2.3 pBar() ============================================================ # == 3.3 sameSpecies() =====================================================
pBar <- function(i, l, nCh = 50) { sameSpecies <- function(a, b) {
# Parameters: a, b two vectors that contain
# binomial species names and maybe additional strain information.
# Value: a boolean vector, true where the species in a is the same as
# the species in b.
# Note: the usual vector recycling applies. Length is not checked.
a <- gsub("^(\\S+\\s\\S+).*", "\\1", a)
b <- gsub("^(\\S+\\s\\S+).*", "\\1", b)
if (any(! grepl("^\\S+\\s\\S+$", a))) {
stop("\"a\" contains elements that are not binomial names.")
}
if (any(! grepl("^\\S+\\s\\S+$", b))) {
stop("\"b\" contains elements that are not binomial names.")
}
return(a == b)
}
# == 3.4 pBar() ============================================================
pBar <- function(i, l, nCh = 50) {
# Draw a progress bar in the console # Draw a progress bar in the console
# i: the current iteration # i: the current iteration
# l: the total number of iterations # l: the total number of iterations
@ -134,7 +165,7 @@ pBar <- function(i, l, nCh = 50) {
} }
# == 2.4 waitTimer() ======================================================= # == 3.5 waitTimer() =======================================================
waitTimer <- function(t, nIntervals = 50) { waitTimer <- function(t, nIntervals = 50) {
# pause and wait for t seconds and display a progress bar as # pause and wait for t seconds and display a progress bar as
# you are waiting # you are waiting
@ -162,7 +193,7 @@ waitTimer <- function(t, nIntervals = 50) {
} }
# == 2.5 fetchMSAmotif() =================================================== # == 3.6 fetchMSAmotif() ===================================================
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. # Biostrings package must be installed.
@ -206,7 +237,7 @@ fetchMSAmotif <- function(ali, mot) {
} }
# == 2.6 H() (Shannon entropy) ============================================= # == 3.7 H() (Shannon entropy) =============================================
H <- function(x, N) { H <- function(x, N) {
# calculate the Shannon entropy of the vector x given N possible states # calculate the Shannon entropy of the vector x given N possible states
# (in bits). # (in bits).
@ -220,9 +251,9 @@ H <- function(x, N) {
# = 3 DATA ================================================================ # = 4 DATA ================================================================
# == 3.1 REFspecies ======================================================== # == 4.1 REFspecies ========================================================
# 10 species of fungi for reference analysis. # 10 species of fungi for reference analysis.
# http://steipe.biochemistry.utoronto.ca/abc/index.php/Reference_species_for_fungi # http://steipe.biochemistry.utoronto.ca/abc/index.php/Reference_species_for_fungi
REFspecies <- c("Aspergillus nidulans", REFspecies <- c("Aspergillus nidulans",
@ -237,10 +268,10 @@ REFspecies <- c("Aspergillus nidulans",
"Wallemia mellicola") "Wallemia mellicola")
# = 4 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS ================================== # = 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS ==================================
# == 4.1 getMYSPE() ======================================================== # == 5.1 getMYSPE() ========================================================
getMYSPE <- function(x) { getMYSPE <- function(x) {
dat <- readRDS("./data/sDat.rds") dat <- readRDS("./data/sDat.rds")
map <- readRDS("./data/MYSPEmap.rds") map <- readRDS("./data/MYSPEmap.rds")
@ -249,7 +280,7 @@ getMYSPE <- function(x) {
} }
# == 4.2 selectPDBrep() ==================================================== # == 5.2 selectPDBrep() ====================================================
selectPDBrep <- function(n, seed) { selectPDBrep <- function(n, seed) {
# Select n PDB IDs from a list of high-resolution, non-homologous, single # Select n PDB IDs from a list of high-resolution, non-homologous, single
# domain, single chain structure files that represent a CATH topology # domain, single chain structure files that represent a CATH topology