add digest:: and jsonlite::, and sameSpecies(),
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.utilities.R
83
.utilities.R
@ -6,7 +6,7 @@
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# Date: 2017-09 - 2020-09
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# Author: Boris Steipe
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#
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# V 1.4 Maintenance
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# V 1.4 Maintenance, and new validation utilities
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# V 1.3.1 prefix Biostrings:: to subseq()
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# V 1.3 load msa support functions
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# V 1.2 update database utilities to support 2017 version of JSON sources
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@ -23,19 +23,21 @@
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#TOC>
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#TOC> Section Title Line
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#TOC> -----------------------------------------------------------
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#TOC> 1 SCRIPTS TO SOURCE 42
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#TOC> 2 SUPPORT FUNCTIONS 49
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#TOC> 2.1 objectInfo() 52
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#TOC> 2.2 biCode() 80
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#TOC> 2.3 pBar() 114
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#TOC> 2.4 waitTimer() 136
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#TOC> 2.5 fetchMSAmotif() 164
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#TOC> 2.6 H() (Shannon entropy) 208
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#TOC> 3 DATA 222
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#TOC> 3.1 REFspecies 224
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#TOC> 4 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS 239
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#TOC> 4.1 getMYSPE() 242
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#TOC> 4.2 selectPDBrep() 251
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#TOC> 1 SCRIPTS TO SOURCE 45
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#TOC> 2 PACKAGES 51
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#TOC> 3 SUPPORT FUNCTIONS 62
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#TOC> 3.1 objectInfo() 65
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#TOC> 3.2 biCode() 93
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#TOC> 3.3 sameSpecies() 127
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#TOC> 3.4 pBar() 146
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#TOC> 3.5 waitTimer() 168
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#TOC> 3.6 fetchMSAmotif() 196
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#TOC> 3.7 H() (Shannon entropy) 240
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#TOC> 4 DATA 254
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#TOC> 4.1 REFspecies 256
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#TOC> 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS 271
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#TOC> 5.1 getMYSPE() 274
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#TOC> 5.2 selectPDBrep() 283
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#TOC>
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#TOC> ==========================================================================
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@ -46,11 +48,21 @@ source("./scripts/ABC-dbUtilities.R")
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source("./scripts/ABC-writeALN.R")
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source("./scripts/ABC-writeMFA.R")
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# = 2 PACKAGES ============================================================
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# = 2 SUPPORT FUNCTIONS ===================================================
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if (! requireNamespace("digest", quietly = TRUE)) {
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install.packages("digest")
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}
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if (! requireNamespace("jsonlite", quietly = TRUE)) {
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install.packages("jsonlite")
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}
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# == 2.1 objectInfo() ======================================================
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# = 3 SUPPORT FUNCTIONS ===================================================
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# == 3.1 objectInfo() ======================================================
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objectInfo <- function(x) {
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# Function to combine various information items about R objects
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#
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@ -78,7 +90,7 @@ objectInfo <- function(x) {
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}
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# == 2.2 biCode() ==========================================================
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# == 3.2 biCode() ==========================================================
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biCode <- function(s) {
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# Make a 5 character "biCode" from a binomial name by concatening
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# the uppercased first three letter of the first word and the first
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@ -112,7 +124,26 @@ biCode <- function(s) {
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}
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# == 2.3 pBar() ============================================================
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# == 3.3 sameSpecies() =====================================================
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sameSpecies <- function(a, b) {
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# Parameters: a, b two vectors that contain
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# binomial species names and maybe additional strain information.
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# Value: a boolean vector, true where the species in a is the same as
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# the species in b.
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# Note: the usual vector recycling applies. Length is not checked.
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a <- gsub("^(\\S+\\s\\S+).*", "\\1", a)
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b <- gsub("^(\\S+\\s\\S+).*", "\\1", b)
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if (any(! grepl("^\\S+\\s\\S+$", a))) {
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stop("\"a\" contains elements that are not binomial names.")
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}
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if (any(! grepl("^\\S+\\s\\S+$", b))) {
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stop("\"b\" contains elements that are not binomial names.")
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}
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return(a == b)
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}
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# == 3.4 pBar() ============================================================
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pBar <- function(i, l, nCh = 50) {
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# Draw a progress bar in the console
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# i: the current iteration
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@ -134,7 +165,7 @@ pBar <- function(i, l, nCh = 50) {
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}
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# == 2.4 waitTimer() =======================================================
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# == 3.5 waitTimer() =======================================================
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waitTimer <- function(t, nIntervals = 50) {
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# pause and wait for t seconds and display a progress bar as
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# you are waiting
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@ -162,7 +193,7 @@ waitTimer <- function(t, nIntervals = 50) {
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}
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# == 2.5 fetchMSAmotif() ===================================================
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# == 3.6 fetchMSAmotif() ===================================================
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fetchMSAmotif <- function(ali, mot) {
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# Retrieve a subset from ali that spans the sequence in mot.
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# Biostrings package must be installed.
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@ -206,7 +237,7 @@ fetchMSAmotif <- function(ali, mot) {
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}
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# == 2.6 H() (Shannon entropy) =============================================
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# == 3.7 H() (Shannon entropy) =============================================
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H <- function(x, N) {
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# calculate the Shannon entropy of the vector x given N possible states
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# (in bits).
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@ -220,9 +251,9 @@ H <- function(x, N) {
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# = 3 DATA ================================================================
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# = 4 DATA ================================================================
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# == 3.1 REFspecies ========================================================
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# == 4.1 REFspecies ========================================================
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# 10 species of fungi for reference analysis.
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# http://steipe.biochemistry.utoronto.ca/abc/index.php/Reference_species_for_fungi
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REFspecies <- c("Aspergillus nidulans",
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@ -237,10 +268,10 @@ REFspecies <- c("Aspergillus nidulans",
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"Wallemia mellicola")
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# = 4 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS ==================================
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# = 5 FUNCTIONS TO CUSTOMIZE ASSIGNMENTS ==================================
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# == 4.1 getMYSPE() ========================================================
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# == 5.1 getMYSPE() ========================================================
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getMYSPE <- function(x) {
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dat <- readRDS("./data/sDat.rds")
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map <- readRDS("./data/MYSPEmap.rds")
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@ -249,7 +280,7 @@ getMYSPE <- function(x) {
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}
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# == 4.2 selectPDBrep() ====================================================
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# == 5.2 selectPDBrep() ====================================================
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selectPDBrep <- function(n, seed) {
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# Select n PDB IDs from a list of high-resolution, non-homologous, single
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# domain, single chain structure files that represent a CATH topology
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