miga-base 1.3.7.0 → 1.3.7.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b5e0216cf49c600ae5776ea4e45bfcc2441ffed928908b20bbfc32541b08351a
-  data.tar.gz: a826116aa5208524e029bd2c6324a89d1805653dd20659a9738e627439192ad1
+  metadata.gz: b57ca3778ff3605473ebae2ebf69aabdb231302a59605094721c6af9cbc7a798
+  data.tar.gz: fbe455bc223b23e5b906874fede98aa85ad443e83d3c0e87839f3bb9bf46ba29
 SHA512:
-  metadata.gz: 8da516f7f72b162e643202d1e84e57646f36afe895f7e57695bb281a937e6a80ee8cdbd333fe83e24f2708d2306e10d9d216adc86c510e07bf2dcdf3a02372d6
-  data.tar.gz: 3cbc31c7152861e678858420e213c35f4283c668586d0770a1d933e6d788589f006de645b9de292bbc991511c72a375bc97881981aa40c412271063b9434c83b
+  metadata.gz: 682cc9964783ebc692be1d8358708d800caa08713b818a9aae7a6ed4d25d0874ddc553ba7e17ce2712092c9e2874353c00b90c3d8f49a3d339a33f42a7cfed6e
+  data.tar.gz: 63e23a79b5af66e4f5816d6ece02b1f349f0477bcf46a2646328028654ffb9792a33c2ddb0e9237571112232c6e735e3a4df8433608495b43be7b6da038651c6

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, 0].freeze
+  VERSION = [1.3, 7, 2].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, 4)
+  VERSION_DATE = Date.new(2023, 6, 15)
 
   ##
   # References of MiGA

data/scripts/aai_distances.bash

@@ -29,17 +29,25 @@ function aai_tsv {
           { if ($1 > $2) { a=$1; $1=$2; $2=a; } } { print $0 }' \
       | sort -k 1,2 -u
   else
-    foreach_database "$SQL"
+    foreach_database_aai
   fi
 }
 
 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)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.7.0
+  version: 1.3.7.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-06-04 00:00:00.000000000 Z
+date: 2023-06-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons