miga-base 0.3.12.0 → 0.3.12.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 48d903a383d237f7b236d8ad1706a5fb017b31d320768353a1bc33846ea0d471
-  data.tar.gz: 9b448f00992aa4152df34ded6a48105afe5c1daf1e994737f253b519f81c998f
+  metadata.gz: 27eb47a34686d0488ec7ea4fd46f1d483b544153e9602770341758053fbbd3d4
+  data.tar.gz: 4dd5dd7d68382191de3e863831d4ceebf36f3fa4aa87e1a3206560c04faf9cf9
 SHA512:
-  metadata.gz: 1579eecdab3c38bda21678baa4c903c85dfbb07e19f993212d89f6b62e1561d4044b41cfc98d80e43780d1fd172ef607a92d5320ff570de87dafda03520f2d59
-  data.tar.gz: d083fc8ae10735f647681d3924c8990951fc2a6ba7d501c10b89d32b0f00088a5128dfca2b24df118b2f8a56e3a5853d210933e300d7ab7bd3bd14c4bab90b8a
+  metadata.gz: c949c82c16dbc89b1ce2b8c7b37a15a18909a554f5ce6bff943f7a881fe1ee5f9d4827f3dea2eb5cb172501df154d7c2608a16444040e09472d38ec9b6b2b0c7
+  data.tar.gz: 33aee8986863e07eec41bc9a139cfa90c036a1bc6c73b70407b46a5dd92d2deff1a794bf9db89f2ffdfec7931b2191c6cf759b9bdc2ae33bec4a19979abb0d98

data/lib/miga/daemon.rb

@@ -240,8 +240,8 @@ class MiGA::Daemon < MiGA::MiGA
       return false
     end
     flush!
-    if loop_i==4
-      say 'Housekeeping for sanity'
+    if loop_i == 12
+      say 'Probing running jobs'
       @loop_i = 0
       purge!
     end

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ 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 = [0.3, 12, 0]
+  VERSION = [0.3, 12, 1]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2019, 04, 26)
+  VERSION_DATE = Date.new(2019, 8, 5)
   
   ##
   # Reference of MiGA.

data/scripts/ogs.bash

@@ -23,6 +23,7 @@ if [[ -n $DS ]] ; then
         [[ -s "$file" ]] && continue
         echo "SELECT seq1,id1,seq2,id2,bitscore from rbm where id >= $MIN_ID;" \
           | sqlite3 "../../09.distances/02.aai/$i.db" | tr "\\|" " " \
+          | perl -pe 's/ gene_/ /g' \
           | awk '{ print $1">"$2"'"\\t"'"$3">"$4"'"\\t"'"$5 }' \
           > "$file.tmp"
         mv "$file.tmp" "$file"
@@ -34,9 +35,9 @@ if [[ -n $DS ]] ; then
     # Estimate OGs and Clean RBMs
     ogs.mcl.rb -o miga-project.ogs --abc miga-project.abc -t "$CORES"
     if [[ $(miga about -P "$PROJECT" -m clean_ogs) == "false" ]] ; then
-      rm miga-project.abc
-    else
       gzip -9 miga-project.abc
+    else
+      rm miga-project.abc
     fi
   fi
 

data/scripts/trimmed_fasta.bash

@@ -31,7 +31,7 @@ if [[ -e "../02.trimmed_reads/$b.2.clipped.fastq" ]] ; then
     > "$b.SingleReads.fa"
   gzip -9 -f "$b.SingleReads.fa"
 else
-   mv "$b.1.fasta" "$b.SingleReads.fa"
+  mv "$b.1.fasta" "$b.SingleReads.fa"
 fi
 
 # Compress input at 01.raw_reads and 02.trimmed_reads

data/test/daemon_test.rb

@@ -58,12 +58,12 @@ class DaemonTest < Test::Unit::TestCase
     end
     assert_equal(Time, d.last_alive.class)
     assert(out.string =~ /-{20}\n.*MiGA:#{p.name} launched/)
-    2.times{ d.in_loop }
-    assert_equal(3, d.loop_i)
+    10.times{ d.in_loop }
+    assert_equal(11, d.loop_i)
     out = capture_stdout do
       d.in_loop
     end
-    assert(out.string =~ /Housekeeping for sanity/)
+    assert(out.string =~ /Probing running jobs/)
     assert_equal(0, d.loop_i)
   end
 
@@ -86,7 +86,7 @@ class DaemonTest < Test::Unit::TestCase
       assert(l[0] =~ /-{20}\n/)
       assert(l[1] =~ /MiGA:#{p.name} launched/)
       assert(l[2] =~ /-{20}\n/)
-      assert(l[3] =~ /Housekeeping for sanity\n/)
+      assert(l[3] =~ /Probing running jobs\n/)
     end
   ensure
     Process.kill("KILL", $child) unless $child.nil?

data/utils/distance/commands.rb

@@ -58,7 +58,7 @@ module MiGA::DistanceRunner::Commands
   # Returns +nil+ otherwise
   def ani_after_aai(target, aai_limit = 85.0)
     aai = aai(target)
-    ani(target) unless aai.nil? or aai < aai_limit
+    (aai.nil? or aai < aai_limit) ? nil : ani(target)
   end
 
   ##

data/utils/enveomics/Scripts/HMM.essential.rb

@@ -255,7 +255,7 @@ begin
             cur_model = nil
             mask = []
           when /^#=GS (\S+)\/([\d\-]+)\s+DE/
-            cur_model ||= genes.rassoc($1).first
+            cur_model ||= ( genes.rassoc($1) || [] ).first
             aln[ cur_model ] ||= [ "# #{cur_model} : #{$1} : #{$2}" ]
           when /^#=GC RF\s+(\S+)/
             aln[ cur_model ][ 1 ] ||= $1.upcase.tap do |i|

data/utils/subclades.R

@@ -111,7 +111,8 @@ subclade_clustering <- function(out_base, thr, ani.d, dist_rdata) {
   
   # Silhouette
   say("Silhouette")
-  k <- 2:min(length(labels(ani.d))-1, 100)
+  nn <- length(labels(ani.d))
+  k <- min(max(floor(0.005 * nn), 2), 20):min(nn-1, 100)
   cl <- makeCluster(thr)
   s <- parSapply(cl, k, function(x) {
       library(cluster)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.12.0
+  version: 0.3.12.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-26 00:00:00.000000000 Z
+date: 2019-08-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons