miga-base 1.3.8.1 → 1.3.8.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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@@ -1,7 +1,7 @@
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@@ -50,8 +50,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
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  # refdb: ['ref-db', 'Check index format of reference databases'],
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  status: ['status', 'Update metadata status of all datasets'],
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  db: ['databases', 'Check integrity of database files'],
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- bidir: ['bidirectional', 'Check distances are bidirectional'],
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  dist: ['distances', 'Check distance summary tables'],
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+ bidir: ['bidirectional', 'Check distances are bidirectional'],
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  files: ['files', 'Check for outdated files'],
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  cds: ['cds', 'Check for gzipped genes and proteins'],
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  ess: ['essential-genes', 'Check for outdated essential genes'],
data/lib/miga/version.rb CHANGED
@@ -12,7 +12,7 @@ module MiGA
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  # - String indicating release status:
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  # - rc* release candidate, not released as gem
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  # - [0-9]+ stable release, released as gem
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- VERSION = [1.3, 8, 1].freeze
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+ VERSION = [1.3, 8, 2].freeze
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  ##
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  # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
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  ##
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  # Date of the current gem relese.
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- VERSION_DATE = Date.new(2023, 7, 5)
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+ VERSION_DATE = Date.new(2023, 8, 8)
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  ##
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  # References of MiGA
data/utils/subclades.R CHANGED
@@ -116,7 +116,8 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
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  say("Subsampling large collection")
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  ids <- sample(labels(ani.d), nMax)
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  ani.d.ori <- ani.d
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- ani.d <- as.dist(as.matrix(ani.d)[ids, ids])
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+ ani.d.m <- as.matrix(ani.d)
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+ ani.d <- as.dist(ani.d.m[ids, ids])
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  }
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  # Silhouette
@@ -157,9 +158,10 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
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  ani.d <- ani.d.ori
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  # Find closest medoid for missing genomes
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  missing <- labels(ani.d)[!labels(ani.d) %in% names(ani.types)]
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- for (i in missing)
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- ani.types[i] <- which.min(as.matrix(ani.d)[ani.medoids, i])
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+ say("- Classify:", length(missing))
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+ for (i in missing) ani.types[i] <- which.min(ani.d.m[ani.medoids, i])
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  # Reorder
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+ say("- Reorder and save")
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  ani.types <- ani.types[labels(ani.d)]
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  # Save missing genomes for inspection
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  write.table(
@@ -190,11 +192,16 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
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  # Generate graphic report
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  say("Graphic report")
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  pdf(paste(out_base, ".pdf", sep = ""), 7, 12)
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- layout(matrix(c(rep(1:3, each = 2), 4:5), byrow = TRUE, ncol = 2))
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- plot_distances(ani.d)
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- plot_silhouette(k, s[1, ], s[2, ], ds, top.n)
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- if (!is.huge) plot_clustering(ani.cl, ani.d, ani.types)
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- if (!is.large) plot_tree(ani.ph, ani.types, ani.medoids)
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+ if (is.huge) {
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+ plot(NULL, axes = FALSE, xlab = '', ylab = '', xlim = 0:1, ylim = 0:1)
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+ legend('center', legend = 'Dataset too large for graphical representation')
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+ } else {
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+ layout(matrix(c(rep(1:3, each = 2), 4:5), byrow = TRUE, ncol = 2))
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+ plot_distances(ani.d)
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+ plot_silhouette(k, s[1, ], s[2, ], ds, top.n)
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+ plot_clustering(ani.cl, ani.d, ani.types)
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+ if (!is.large) plot_tree(ani.ph, ani.types, ani.medoids)
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+ }
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  dev.off()
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  # Save results
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: miga-base
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  version: !ruby/object:Gem::Version
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- version: 1.3.8.1
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+ version: 1.3.8.2
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  platform: ruby
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  authors:
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  - Luis M. Rodriguez-R
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2023-07-05 00:00:00.000000000 Z
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+ date: 2023-08-08 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: daemons