miga-base 1.3.8.1 → 1.3.9.0
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- checksums.yaml +4 -4
- data/README.md +2 -2
- data/lib/miga/cli/action/add_result.rb +22 -1
- data/lib/miga/cli/action/browse/about.html +4 -2
- data/lib/miga/cli/action/doctor.rb +1 -1
- data/lib/miga/cli/action/download/gtdb.rb +1 -1
- data/lib/miga/cli/action/download/ncbi.rb +43 -68
- data/lib/miga/cli/action/download/seqcode.rb +1 -2
- data/lib/miga/cli/action/ncbi_get.rb +1 -8
- data/lib/miga/cli/action/wf.rb +15 -6
- data/lib/miga/cli/objects_helper.rb +3 -0
- data/lib/miga/cli/opt_helper.rb +8 -2
- data/lib/miga/common/net.rb +100 -18
- data/lib/miga/dataset/base.rb +40 -12
- data/lib/miga/dataset/hooks.rb +8 -0
- data/lib/miga/dataset/result/ignore.rb +14 -2
- data/lib/miga/dataset/type.rb +51 -0
- data/lib/miga/dataset.rb +3 -22
- data/lib/miga/json.rb +9 -0
- data/lib/miga/project/base.rb +15 -9
- data/lib/miga/project.rb +7 -1
- data/lib/miga/remote_dataset/base.rb +117 -36
- data/lib/miga/remote_dataset/download.rb +121 -54
- data/lib/miga/remote_dataset.rb +34 -13
- data/lib/miga/result/stats.rb +2 -0
- data/lib/miga/result/versions.rb +23 -0
- data/lib/miga/result.rb +7 -1
- data/lib/miga/taxonomy/base.rb +3 -2
- data/lib/miga/version.rb +2 -2
- data/scripts/assembly.bash +15 -1
- data/scripts/cds.bash +9 -3
- data/scripts/distances.bash +103 -5
- data/scripts/essential_genes.bash +14 -1
- data/scripts/mytaxa.bash +18 -3
- data/scripts/mytaxa_scan.bash +16 -3
- data/scripts/read_quality.bash +6 -2
- data/scripts/ssu.bash +19 -1
- data/scripts/stats.bash +9 -3
- data/scripts/taxonomy.bash +98 -2
- data/scripts/trimmed_fasta.bash +10 -2
- data/scripts/trimmed_reads.bash +26 -6
- data/test/dataset_test.rb +17 -2
- data/test/hook_test.rb +3 -2
- data/test/net_test.rb +21 -5
- data/test/project_test.rb +13 -0
- data/test/remote_dataset_test.rb +106 -7
- data/test/result_test.rb +47 -21
- data/test/taxonomy_test.rb +9 -3
- data/utils/distance/runner.rb +3 -1
- data/utils/distances.rb +1 -1
- data/utils/subclades.R +15 -8
- metadata +4 -2
data/utils/subclades.R
CHANGED
@@ -116,7 +116,8 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
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|
116
116
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say("Subsampling large collection")
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117
117
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ids <- sample(labels(ani.d), nMax)
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118
118
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ani.d.ori <- ani.d
|
119
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-
ani.d <- as.
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119
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+
ani.d.m <- as.matrix(ani.d)
|
120
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+
ani.d <- as.dist(ani.d.m[ids, ids])
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120
121
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}
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121
122
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122
123
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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
158
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ani.d <- ani.d.ori
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158
159
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# Find closest medoid for missing genomes
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159
160
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missing <- labels(ani.d)[!labels(ani.d) %in% names(ani.types)]
|
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))
|
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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164
166
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# Save missing genomes for inspection
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165
167
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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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190
192
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# Generate graphic report
|
191
193
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say("Graphic report")
|
192
194
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pdf(paste(out_base, ".pdf", sep = ""), 7, 12)
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193
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-
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194
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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) {
|
196
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+
plot(NULL, axes = FALSE, xlab = '', ylab = '', xlim = 0:1, ylim = 0:1)
|
197
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+
legend('center', legend = 'Dataset too large for graphical representation')
|
198
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+
} else {
|
199
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+
layout(matrix(c(rep(1:3, each = 2), 4:5), byrow = TRUE, ncol = 2))
|
200
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+
plot_distances(ani.d)
|
201
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+
plot_silhouette(k, s[1, ], s[2, ], ds, top.n)
|
202
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+
plot_clustering(ani.cl, ani.d, ani.types)
|
203
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+
if (!is.large) plot_tree(ani.ph, ani.types, ani.medoids)
|
204
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+
}
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198
205
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dev.off()
|
199
206
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200
207
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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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2
2
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name: miga-base
|
3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 1.3.
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4
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+
version: 1.3.9.0
|
5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Luis M. Rodriguez-R
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8
8
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autorequire:
|
9
9
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bindir: bin
|
10
10
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cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2024-01-22 00:00:00.000000000 Z
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12
12
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dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
|
14
14
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name: daemons
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@@ -218,6 +218,7 @@ files:
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218
218
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- lib/miga/dataset/result/add.rb
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219
219
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- lib/miga/dataset/result/ignore.rb
|
220
220
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- lib/miga/dataset/status.rb
|
221
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+
- lib/miga/dataset/type.rb
|
221
222
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- lib/miga/json.rb
|
222
223
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- lib/miga/lair.rb
|
223
224
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- lib/miga/metadata.rb
|
@@ -235,6 +236,7 @@ files:
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235
236
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- lib/miga/result/dates.rb
|
236
237
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- lib/miga/result/source.rb
|
237
238
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- lib/miga/result/stats.rb
|
239
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+
- lib/miga/result/versions.rb
|
238
240
|
- lib/miga/sqlite.rb
|
239
241
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- lib/miga/tax_dist.rb
|
240
242
|
- lib/miga/tax_index.rb
|