miga-base 0.7.12.2 → 0.7.13.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA256:
-  metadata.gz: c57b841cc84841ebfd868af862204179e443d37eb4ec5550ea9ef7df63b9d933
-  data.tar.gz: 5512fe8305c2b6193f5d1a5c99e663ef480be32db2e8bdc7087826bdeeae5b35
+SHA1:
+  metadata.gz: 964b803e09887476153335589fad3d5aee2861ea
+  data.tar.gz: ee0d34a4a7c8569d39bea4855a6054c57de78c81
 SHA512:
-  metadata.gz: 63e095dded680c2a6d1519d8fc8788d4d44cf523fc84b9e67ee453dffb9f05c75e2acafc283b511f6b27638e678d53f7362b056f35d18d5b08893419c7d24302
-  data.tar.gz: efac7f7c3d65640b64dc6d9b32e3bd520faebda05a72f1b88a2ee4c11546b5366db1ac42ea296ba73fe1f7873244a9f64791a180c9094a374a7ebbf1c589d491
+  metadata.gz: b84efbc94fbfc848b85ae7c3cca7e26f2baea74c5f066a63cf1ede7fb26ed6c634f4c2e2cbe1c2752e54624cf48d6597b933474d4b4d6083cb505a3b17063cf5
+  data.tar.gz: 0c7cfc6a149cab5fa1cfc5e386de789f84c132d227ad8ebbbc42dee2b076010bfe06b6697e69efe00a6639283c472f9ca3793a1e113506e691e50a182cfee2c6

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

@@ -27,10 +27,13 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
         '--threshold FLOAT', Float,
         "Metric threshold (%) to dereplicate. By default: #{cli[:threshold]}"
       ) { |v| cli[:threshold] = v }
+      opt.on(
+        '--quality',
+        'Use genome with highest quality as clade representatives (default)'
+      ) { |v| cli[:criterion] = :quality }
       opt.on(
         '--medoids',
-        'Use medoids as clade representatives',
-        'By default: Use genome with the highest quality'
+        'Use medoids as clade representatives'
       ) { |v| cli[:criterion] = :medoids }
       opt.on(
         '--no-collection',
@@ -47,12 +50,18 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
 
   def perform
     # Input data
-    p = create_project(:assembly,
-                       { run_project_stats: false, run_clades: false,
-                         gsp_metric: cli[:metric], :"gsp_#{cli[:metric]}" => cli[:threshold] },
-                       { run_mytaxa_scan: false, run_ssu: false })
+    p = create_project(
+      :assembly,
+      {
+        run_project_stats: false,
+        run_clades: false,
+        gsp_metric: cli[:metric],
+        :"gsp_#{cli[:metric]}" => cli[:threshold]
+      },
+      { run_mytaxa_scan: false, run_ssu: false }
+    )
     unless cli[:threshold] >= 0.0 && cli[:threshold] <= 100.0
-      raise "The threshold of identity must be in the range [0,100]"
+      raise 'The threshold of identity must be in the range [0,100]'
     end
 
     # Run
@@ -65,8 +74,8 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
   private
 
   def dereplicate(p)
-    cli.say "Extracting genomospecies clades"
-    r = p.result(:clade_finding) or raise "Result unavailable: run failed"
+    cli.say 'Extracting genomospecies clades'
+    r = p.result(:clade_finding) or raise 'Result unavailable: run failed'
     c_f = r.file_path(:clades_gsp) or raise 'Result incomplete: run failed'
     clades = File.readlines(c_f).map { |i| i.chomp.split("\t") }
     rep = representatives(p)
@@ -87,7 +96,7 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
   end
 
   def representatives(p)
-    cli.say "Identifying representatives"
+    cli.say 'Identifying representatives'
     f = File.expand_path('representatives.txt', cli[:outdir])
     if cli[:criterion] == :medoids
       FileUtils.cp(p.result(:clade_finding).file_path(:medoids_gsp), f)

data/lib/miga/daemon.rb

@@ -91,7 +91,8 @@ class MiGA::Daemon < MiGA::MiGA
     flush!
     if (loop_i % 12).zero?
       purge!
-      recalculate_status!
+      # TEMPORARILY DISABLED:
+      # recalculate_status!
     end
     save_status
     sleep(latency)

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 12, 2]
+  VERSION = [0.7, 13, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 7, 24)
+  VERSION_DATE = Date.new(2020, 7, 31)
 
   ##
   # Reference of MiGA.

data/scripts/aai_distances.bash

@@ -13,17 +13,20 @@ echo -n "" > miga-project.log
 DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
 
 # Extract values
-echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
-for i in $DS ; do
-  echo "SELECT CASE WHEN omega!=0 THEN 'AAI' ELSE 'hAAI_AAI' END," \
-    " seq1, seq2, aai, sd, n, omega from aai;" \
-    | sqlite3 "$i.db" | tr "\\|" "\\t" >>miga-project.txt
-  echo "$i" >> miga-project.log
-done
+rm -f miga-project.txt
+(
+  echo "metric a b value sd n omega" | tr " " "\\t"
+  for i in $DS ; do
+    echo "SELECT CASE WHEN omega!=0 THEN 'AAI' ELSE 'hAAI_AAI' END," \
+      " seq1, seq2, aai, sd, n, omega from aai;" \
+      | sqlite3 "$i.db" | tr "\\|" "\\t"
+    echo "$i" >> miga-project.log
+  done
+) | gzip -9c > miga-project.txt.gz
 
 # R-ify
 echo "
-aai <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
+aai <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
 save(aai, file='miga-project.Rdata');
 if(sum(aai[,'a'] != aai[,'b']) > 0){
   h <- hist(aai[aai[,'a'] != aai[,'b'], 'value'], breaks=100, plot=FALSE);
@@ -35,9 +38,6 @@ if(sum(aai[,'a'] != aai[,'b']) > 0){
 }
 " | R --vanilla
 
-# Gzip
-gzip -9 -f miga-project.txt
-
 # Finalize
 miga date > "miga-project.done"
 miga add_result -P "$PROJECT" -r "$SCRIPT" -f

data/scripts/ani_distances.bash

@@ -13,16 +13,19 @@ echo -n "" > miga-project.log
 DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
 
 # Extract values
-echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
-for i in $DS ; do
-  echo "SELECT 'ANI', seq1, seq2, ani, sd, n, omega from ani ;" \
-    | sqlite3 "$i.db" | tr "\\|" "\\t" >>miga-project.txt
-  echo "$i" >> miga-project.log
-done
+rm -f miga-project.txt
+(
+  echo "metric a b value sd n omega" | tr " " "\\t"
+  for i in $DS ; do
+    echo "SELECT 'ANI', seq1, seq2, ani, sd, n, omega from ani ;" \
+      | sqlite3 "$i.db" | tr "\\|" "\\t"
+    echo "$i" >> miga-project.log
+  done
+) | gzip -9c > miga-project.txt.gz
 
 # R-ify
 echo "
-ani <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
+ani <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
 save(ani, file='miga-project.Rdata');
 if(sum(ani[,'a'] != ani[,'b']) > 0){
   h <- hist(ani[ani[,'a'] != ani[,'b'], 'value'], breaks=100, plot=FALSE);
@@ -34,9 +37,6 @@ if(sum(ani[,'a'] != ani[,'b']) > 0){
 }
 " | R --vanilla
 
-# Gzip
-gzip -9 -f miga-project.txt
-
 # Finalize
 miga date > "miga-project.done"
 miga add_result -P "$PROJECT" -r "$SCRIPT" -f

data/scripts/haai_distances.bash

@@ -17,30 +17,30 @@ echo -n "" > miga-project.log
 DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
 
 # Extract values
-echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
-for i in $DS ; do
-  echo "SELECT 'hAAI', seq1, seq2, aai, sd, n, omega from aai ;" \
-    | sqlite3 "$i.db" | tr "\\|" "\\t" >>miga-project.txt
-  echo "$i" >> miga-project.log
-done
+rm -f miga-project.txt
+(
+  echo "metric a b value sd n omega" | tr " " "\\t"
+  for i in $DS ; do
+    echo "SELECT 'hAAI', seq1, seq2, aai, sd, n, omega from aai ;" \
+      | sqlite3 "$i.db" | tr "\\|" "\\t"
+    echo "$i" >> miga-project.log
+  done
+) | gzip -9c > miga-project.txt.gz
 
 # R-ify
 echo "
-haai <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
+haai <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
 save(haai, file='miga-project.Rdata');
 if(sum(haai[,'a'] != haai[,'b']) > 0){
   h <- hist(haai[haai[,'a'] != haai[,'b'], 'value'], breaks=100, plot=FALSE);
   write.table(
     cbind(h[['breaks']][-length(h[['breaks']])],
-      h[['breaks']][-1],h[['counts']]),
+      h[['breaks']][-1], h[['counts']]),
     file='miga-project.hist', quote=FALSE, sep='\\t',
     col.names=FALSE, row.names=FALSE);
 }
 " | R --vanilla
 
-# Gzip
-gzip -9 -f miga-project.txt
-
 # Finalize
 miga date > "miga-project.done"
 miga add_result -P "$PROJECT" -r "$SCRIPT" -f

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.12.2
+  version: 0.7.13.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-07-24 00:00:00.000000000 Z
+date: 2020-07-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -560,7 +560,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
+rubyforge_project:
+rubygems_version: 2.5.2.3
 signing_key:
 specification_version: 4
 summary: MiGA