miga-base 1.3.7.1 → 1.3.7.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f740c598f74345dd627aefddf7da473a406f2c5a745ffe455383d87b04ff3840
-  data.tar.gz: 2964b0d1b4c5aecd4c77ad80a0e7399767142c3e99e17c1d2b23f0540e4cb741
+  metadata.gz: da6f90e73e7f3f740623ad77e09886b1c7618de2f484ba412e53d329fb771c12
+  data.tar.gz: 662eda2643f1695285e02ef18076aa3c3bed86bfbbd2d0fc9c91481fbe6fb384
 SHA512:
-  metadata.gz: e932dc0117e9cd6f023ae86ba02970c6e0516ed313fc79ca15045490c3dbc284737c945dd7a599188f73f7d00f50058eecb7c72f5447f9fe5a568c8301fff306
-  data.tar.gz: 857925d63d80c03856229a030252717bce7953222844220db2220e72529a0378b596a2b742273b4abaca078877efa1972b82b4fed5b2939ff21c8f5ee9fbdbe8
+  metadata.gz: 268833ab588449626fd9ee1c8374daea22482fe85d73570c6c9bec58dd1b00c8385e53f8c9d26f0903cf88451f715194c2ddd5bb330eff0a5695ffb9f0bcb51f
+  data.tar.gz: 1dabe6af4158fbb26c760aa2c4673d1cdba45b832a54eb01995418bf11a8cb7c02708e99c54a1862d9bf501101f0fc55afc6f9b44d487c37d7d35cd61a1ff688

data/lib/miga/cli/action/rm.rb

@@ -17,7 +17,7 @@ class MiGA::Cli::Action::Rm < MiGA::Cli::Action
   end
 
   def perform
-    if r = cli.load_result
+    if cli[:result] && r = cli.load_result
       cli[:remove] ? r.remove! : r.unlink
     elsif d = cli.load_dataset
       cli.load_project.unlink_dataset(d.name)

data/lib/miga/result/stats.rb

@@ -208,7 +208,7 @@ module MiGA::Result::Stats
         next if (no += 1) < 4
         stats[:trna_count] += 1
         row = ln.chomp.split("\t")
-        next if row[9] == 'pseudo' || row[4] == 'Undet'
+        next if row[9] == 'pseudo' || %w[Undet Sup].include?(row[4])
         aa[row[4].gsub(/^[a-z]?([A-Za-z]+)[0-9]?/, '\1')] = true
       end
       stats[:trna_aa] = aa.size

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 7, 1].freeze
+  VERSION = [1.3, 7, 3].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 6, 7)
+  VERSION_DATE = Date.new(2023, 6, 29)
 
   ##
   # References of MiGA

data/scripts/aai_distances.bash

@@ -34,12 +34,20 @@ function aai_tsv {
 }
 
 rm -f "miga-project.txt"
-aai_tsv | gzip -9c > "miga-project.txt.gz"
+aai_tsv | tee >(wc -l | awk '{print $1-1}' > "miga-project.txt.lno") \
+  | gzip -9c > "miga-project.txt.gz"
+LNO=$(cat "miga-project.txt.lno")
+rm "miga-project.txt.lno"
 
 # R-ify
 cat <<R | R --vanilla
 file <- gzfile("miga-project.txt.gz")
-aai <- read.table(file, sep = "\t", header = TRUE, as.is = TRUE)
+aai <- read.table(
+  file, sep = "\t", header = TRUE, as.is = TRUE, quote = "",
+  stringsAsFactors = FALSE, comment.char = "", nrows = $LNO,
+  colClasses = c("character", "character",
+                 "numeric", "numeric", "integer", "integer")
+)
 saveRDS(aai, file = "miga-project.rds")
 if(sum(aai[, "a"] != aai[, "b"]) > 0) {
   h <- hist(aai[aai[, "a"] != aai[, "b"], "value"], breaks = 100, plot = FALSE)

data/scripts/ani_distances.bash

@@ -10,20 +10,36 @@ DIR="$PROJECT/data/09.distances/03.ani"
 miga_start_project_step "$DIR"
 
 # Extract values
-rm -f miga-project.txt
-SQL="SELECT seq1, seq2, ani, sd, n, omega from ani;"
-DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
-(
-  echo "a b value sd n omega" | tr " " "\\t"
-  for i in $DS ; do
-    echo "$SQL" | sqlite3 "$DIR/$i.db" | tr "\\|" "\\t"
+function foreach_database_ani {
+  local SQL="SELECT seq1, seq2, ani, sd, n, omega from ani;"
+  local k=0
+  while [[ -n ${DS[$k]} ]] ; do
+    echo "$SQL" | sqlite3 "$DIR/${DS[$k]}.db" | tr "\\|" "\\t"
+    let k=$k+1
   done
-) | gzip -9c > miga-project.txt.gz
+}
+
+function ani_tsv {
+  DS=($(miga ls -P "$PROJECT" --ref --no-multi --active))
+  echo "a b value sd n omega" | tr " " "\\t"
+  foreach_database_ani
+}
+
+rm -f "miga-project.txt"
+ani_tsv | tee >(wc -l | awk '{print $1-1}' > "miga-project.txt.lno") \
+  | gzip -9c > "miga-project.txt.gz"
+LNO=$(cat "miga-project.txt.lno")
+rm "miga-project.txt.lno"
 
 # R-ify
 cat <<R | R --vanilla
 file <- gzfile("miga-project.txt.gz")
-ani <- read.table(file, sep = "\t", header = TRUE, as.is = TRUE)
+ani <- read.table(
+  file, sep = "\t", header = TRUE, as.is = TRUE, quote = "",
+  stringsAsFactors = FALSE, comment.char = "", nrows = $LNO,
+  colClasses = c("character", "character",
+                 "numeric", "numeric", "integer", "integer")
+)
 saveRDS(ani, file = "miga-project.rds")
 if(sum(ani[, "a"] != ani[, "b"]) > 0) {
   h <- hist(ani[ani[, "a"] != ani[, "b"], "value"], breaks = 100, plot = FALSE)

data/utils/subclades.R

@@ -311,7 +311,7 @@ ani_distance <- function (ani_file, sel) {
     sim <- read.table(gzfile(ani_file), sep = "\t", header = TRUE, as.is = TRUE)
   }
   
-  # If there is not data end process
+  # If there is no data, end process
   if (nrow(sim) == 0) return(NULL)
 
   # Apply filter (if requested)
@@ -319,7 +319,7 @@ ani_distance <- function (ani_file, sel) {
   if (!is.na(sel) && file.exists(sel)) {
     say("Filter selection")
     ids <- read.table(sel, sep = "\t", head = FALSE, as.is = TRUE)[,1]
-    sim <- sim[sim$a %in% ids & sim$b %in% ids, ]
+    sim <- sim[which(sim$a %in% ids & sim$b %in% ids), ]
   } else {
     ids <- with(sim, unique(c(a, b)))
   }
@@ -329,7 +329,7 @@ ani_distance <- function (ani_file, sel) {
   sim$d <- 1 - (sim$value / 100)
   return(as.dist(with(sim, {
     out <- matrix(
-      max(d) * 1.2, nrow = length(ids), ncol = length(ids),
+      min(max(d) * 1.2, 1.0), nrow = length(ids), ncol = length(ids),
       dimnames = list(ids, ids)
     )
     out[cbind(ids, ids)] <- 0

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.7.1
+  version: 1.3.7.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-06-07 00:00:00.000000000 Z
+date: 2023-06-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons