miga-base 1.3.8.1 → 1.3.8.2
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- checksums.yaml +4 -4
- data/lib/miga/cli/action/doctor.rb +1 -1
- data/lib/miga/version.rb +2 -2
- data/utils/subclades.R +15 -8
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 2e4abdd418e396b20fcfea4beaf4d70f3b0022808714478581e2e1f6f8a85478
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4
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+
data.tar.gz: 881884c4d5a933b64ac29e93397b62b7d1dc30fd599baaa8b6ac04a3ad3ab051
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 317022ffe39818af13d36e3bf1e1adea80b3ab3aafb265b3df6371b6b5e87efdb75199cf8bd22aea37a63e941f824d1686f85bdb7a38eda3f4ba2a76c535b86b
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7
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+
data.tar.gz: 0d42dadd982374f0c618d76fc030f5665075e9973ca8e8615c5b090ab1dcc6bf663901a8f7355ce3bfa6874941d9098957d31704b6369474e516dd5ebf8c0b6b
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@@ -50,8 +50,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
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50
50
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# refdb: ['ref-db', 'Check index format of reference databases'],
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51
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status: ['status', 'Update metadata status of all datasets'],
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52
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db: ['databases', 'Check integrity of database files'],
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53
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-
bidir: ['bidirectional', 'Check distances are bidirectional'],
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54
53
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dist: ['distances', 'Check distance summary tables'],
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54
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+
bidir: ['bidirectional', 'Check distances are bidirectional'],
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55
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files: ['files', 'Check for outdated files'],
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56
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cds: ['cds', 'Check for gzipped genes and proteins'],
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ess: ['essential-genes', 'Check for outdated essential genes'],
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data/lib/miga/version.rb
CHANGED
@@ -12,7 +12,7 @@ module MiGA
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12
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# - String indicating release status:
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13
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# - rc* release candidate, not released as gem
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14
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# - [0-9]+ stable release, released as gem
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15
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-
VERSION = [1.3, 8,
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15
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+
VERSION = [1.3, 8, 2].freeze
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16
16
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##
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# Nickname for the current major.minor version.
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@@ -20,7 +20,7 @@ module MiGA
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20
20
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21
21
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##
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# Date of the current gem relese.
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23
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-
VERSION_DATE = Date.new(2023,
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23
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+
VERSION_DATE = Date.new(2023, 8, 8)
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24
24
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25
25
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##
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26
26
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# References of MiGA
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data/utils/subclades.R
CHANGED
@@ -116,7 +116,8 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
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116
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say("Subsampling large collection")
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117
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ids <- sample(labels(ani.d), nMax)
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118
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ani.d.ori <- ani.d
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119
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-
ani.d <- as.
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119
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+
ani.d.m <- as.matrix(ani.d)
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120
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+
ani.d <- as.dist(ani.d.m[ids, ids])
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120
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}
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# Silhouette
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@@ -157,9 +158,10 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
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157
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ani.d <- ani.d.ori
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158
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# Find closest medoid for missing genomes
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159
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missing <- labels(ani.d)[!labels(ani.d) %in% names(ani.types)]
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160
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-
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161
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-
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161
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+
say("- Classify:", length(missing))
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162
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+
for (i in missing) ani.types[i] <- which.min(ani.d.m[ani.medoids, i])
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162
163
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# Reorder
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164
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+
say("- Reorder and save")
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163
165
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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(
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@@ -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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-
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-
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195
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-
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196
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-
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197
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-
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195
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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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197
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legend('center', legend = 'Dataset too large for graphical representation')
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} else {
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199
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layout(matrix(c(rep(1:3, each = 2), 4:5), byrow = TRUE, ncol = 2))
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200
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+
plot_distances(ani.d)
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201
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plot_silhouette(k, s[1, ], s[2, ], ds, top.n)
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202
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plot_clustering(ani.cl, ani.d, ani.types)
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203
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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
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: miga-base
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3
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version: !ruby/object:Gem::Version
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4
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-
version: 1.3.8.
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4
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+
version: 1.3.8.2
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platform: ruby
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6
6
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authors:
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- Luis M. Rodriguez-R
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8
8
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autorequire:
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9
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bindir: bin
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10
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cert_chain: []
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11
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-
date: 2023-
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11
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+
date: 2023-08-08 00:00:00.000000000 Z
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12
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dependencies:
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13
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- !ruby/object:Gem::Dependency
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14
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name: daemons
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