miga-base 1.2.11.0 → 1.2.12.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: bca3141b79964a880f22ba6e4e724b4821466321942a02f6443dcb1e5ba3b6cc
-  data.tar.gz: 45af5251d8bced591ba493ca7b9cac5ae45d2c527f19902773a122f436b93808
+  metadata.gz: 176a9a20427a4b14db0418fb1140025d2a5dc3737e4e6c55926524bd4d0f4d32
+  data.tar.gz: 4d1dca0ba71ea2ad86f4a4ffe5fbda8a8146f91464f092efe780ba92598bfd36
 SHA512:
-  metadata.gz: 7e648e5f3068348bd0064f8c3f8e3691c9c978aa9c06bb35bcf1b9a3b9a8d8eb0d1d67b5520e52537cf3ef6940414f88d24602cfaa47129fa39face66a95b375
-  data.tar.gz: aab0fb4e5764d76eb78a908e6997761e346d8027323bf305528ccf5abcd258b3b84d6ef356352a270b2e273e8563a28e6e9e0f6993bd7bd648ac28c4a6bce6d7
+  metadata.gz: 521cb14499220bcf5cec8d5a532f7e8fe2708eac6ca7bdd53e5ca5472857d0a57f08750a232cbbd2cf704b082295a6668ec275e0956fc08a783dda13b0cc0471
+  data.tar.gz: 451d7f35d2e1666b3125fa58a85c171eb89310379a6acd67c1fd19bb0e1274e1cfe0a93775ccf42e93f03ea5f0e85b6045147fc8272b0d26e57bfdb97ecfa623

data/lib/miga/cli/action/download/gtdb.rb

@@ -28,7 +28,6 @@ module MiGA::Cli::Action::Download::Gtdb
 
   def remote_list
     cli.say 'Downloading genome list'
-    ds = {}
     extra = ['sp_reps_only=' + cli[:reference].to_s]
     json = MiGA::RemoteDataset.download(
       :gtdb, :taxon, cli[:taxon], :genomes, nil, extra
@@ -49,7 +48,7 @@ module MiGA::Cli::Action::Download::Gtdb
   end
 
   def remote_row_name(asm)
-    acc = "#{asm}"
+    acc = asm.to_s
     acc.gsub!(/\.\d+\Z/, '') unless cli[:add_version]
     acc.miga_name
   end

data/lib/miga/cli/objects_helper.rb

@@ -99,6 +99,9 @@ module MiGA::Cli::ObjectsHelper
         when 'true';  v = true
         when 'false'; v = false
         when 'nil';   v = nil
+        when /^(Int|Float)\(.*\)$/
+          tr = v =~ /^Int/ ? :to_i : :to_f
+          v = v.gsub(/.*\((.*)\)/, '\1').send(tr)
         end
         if k == '_step'
           obj.metadata["_try_#{v}"] ||= 0

data/lib/miga/dataset/result.rb

@@ -384,7 +384,10 @@ module MiGA::Dataset::Result
   ##
   # Add result type +:stats+ at +base+ (no +_opts+ supported)
   def add_result_stats(base, _opts)
-    MiGA::Result.new("#{base}.json")
+    add_files_to_ds_result(
+      MiGA::Result.new("#{base}.json"), name,
+      trna_list: '.trna.txt'
+    )
   end
 
   ##

data/lib/miga/taxonomy.rb

@@ -63,6 +63,8 @@ class MiGA::Taxonomy < MiGA::MiGA
     @ranks[rank.to_sym]
   end
 
+  alias :fetch :[]
+
   ##
   # Get the alternative taxonomies.
   # - If +which+ is nil (default), returns all alternative taxonomies as Array

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 = [1.2, 11, 0].freeze
+  VERSION = [1.2, 12, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2022, 12, 28)
+  VERSION_DATE = Date.new(2022, 12, 30)
 
   ##
   # References of MiGA

data/scripts/stats.bash

@@ -9,7 +9,32 @@ DIR="$PROJECT/data/90.stats"
 cd "$DIR"
 
 # Initialize
-miga date > "$DATASET.start"
+miga date > "${DATASET}.start"
+
+# tRNAscan-SE
+fa="../05.assembly/${DATASET}.LargeContigs.fna"
+if [[ -s "$fa" ]] ; then
+  d="$(miga ls -P "$PROJECT" -D "$DATASET" -m tax:d | awk '{print $2}')"
+  if [[ "$d" == "Bacteria" || "$d" == "Archaea" || "$d" == "Eukaryota" ]] ; then
+    dom_opt="-$(echo "$d" | perl -pe 's/(\S).*/$1/')"
+    out="${DATASET}.trna.txt"
+    # `echo O` is to avoid a hang from a pre-existing output file.
+    # This is better than pre-checking (and removing), because it avoids
+    # the (unlikely) scenario of a file racing (e.g., a file created right
+    # before tRNAscan-SE starts, or a `rm` failure).
+    #
+    # The trailing `|| true` is to treat failure as non-fatal
+    echo O | tRNAscan-SE $dom_opt -o "$out" -q "$fa" || true
+    if [[ -s "$out" ]] ; then
+      cnt=$(tail -n +4 "$out" | wc -l | awk '{print $1}')
+      aa="$(tail -n +4 "$out" | grep -v 'pseudo$' | awk '{print $5}' \
+               | grep -v 'Undet' | perl -pe 's/^f?([A-Za-z]+)[0-9]?/$1/' \
+               | sort | uniq | wc -l | awk '{print $1}')"
+      miga edit -P "$PROJECT" -D "$DATASET" \
+        -m "trna_count=Int($cnt),trna_aa=Int($aa)"
+    fi
+  fi
+fi
 
 # Calculate statistics
 for i in raw_reads trimmed_fasta assembly cds essential_genes ssu distances taxonomy ; do

data/utils/requirements.txt

@@ -20,3 +20,4 @@ Fastp (reads)	fastp		https://github.com/OpenGene/fastp
 Temurin (rdp)	java		https://adoptium.net/				Any Java VM would work
 MyTaxa (mytaxa)	MyTaxa		http://enve-omics.ce.gatech.edu/mytaxa
 Krona (mytaxa)	ktImportText	https://github.com/marbl/Krona/wiki
+tRNAscan-SE	tRNAscan-SE	http://trna.ucsc.edu/tRNAscan-SE/		Required version: 2+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.11.0
+  version: 1.2.12.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-12-28 00:00:00.000000000 Z
+date: 2022-12-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons