miga-base 0.2.2.2 → 0.2.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 569b4e7cff6063f23d5c76445ce5fe8379c152bd
-  data.tar.gz: 9ea1a8bff35874d39a27eb0544e4f9b262441368
+  metadata.gz: 08a4a7fe880fa3b6653122e96d4e25fc39832020
+  data.tar.gz: 9a154fe5ec29b9b4bcb56cf01f11eb9a5ce77e3a
 SHA512:
-  metadata.gz: 0eda211778880b2dcaca0b5504ce560aeed3f7f4d420e0c127019ce86f68511e67af329aa920ab0816460c8730eed8cb0f46f6b12debf637ce8e95891d670cf0
-  data.tar.gz: 22d7016022c1d63d848b8046ca8899dbf95bf22fa132613783f9c1b72ca0e289e1ce653a5b300824eeb64697354bbdbc705950db8b147604e38318e0456811d6
+  metadata.gz: 19b8971dca597bc26a30cefc6b4c9973774a54cfd104ca5f45c8cea844205a01f58370556457426621009e7c7bfbc1c3f28afad93ff76fe818514b392b1fcaa0
+  data.tar.gz: ed05189ab71cbe8f8721dd7b584441cc3bf338a2746be46a08aeb1550545a9261c5d86f4d7133f99c5b6d4237fe975353832d7516400cbd1e3c037aef8d6bf38

data/actions/create_dataset.rb

@@ -23,6 +23,22 @@ OptionParser.new do |opt|
   opt.on("--update",
     "Updates the dataset if it already exists."){ o[:update]=true }
   opt_common(opt, o)
+  opt.separator ""
+  opt.separator "External input data"
+  opt.on("--raw-reads FILE1,FILE2", Array,
+    "Comma-delimited paths to the raw reads in FastQ format.",
+    "One file is assumed to be single reads, two are assumed to be paired."
+    ){ |v| o[:raw_reads] = v }
+  opt.on("--trimmed-fasta-single FILE", Array,
+    "Path to the single trimmed reads in FastA format."
+    ){ |v| o[:trimmed_fasta_s] = v }
+  opt.on("--trimmed-fasta-coupled FILE1,FILE2", Array,
+    "Comma-delimited paths to the coupled trimmed reads in FastA format.",
+    "One file is assumed to be interposed, two are assumed to contain sisters."
+    ){ |v| o[:trimmed_fasta_c] = v }
+  opt.on("--assembly FILE", Array,
+    "Path to the contigs (or scaffolds) of the assembly in FastA format."
+    ){ |v| o[:assembly] = v }
 end.parse!
 
 ##=> Main <=
@@ -38,16 +54,39 @@ $stderr.puts "Loading dataset." unless o[:q]
 d = o[:update] ? p.dataset(o[:dataset]) :
   MiGA::Dataset.new(p, o[:dataset], o[:ref], {})
 raise "Dataset does not exist." if d.nil?
+
+in_files = [:raw_reads, :trimmed_fasta_s, :trimmed_fasta_c, :assembly]
+def cp_result(o, d, p, sym, res_sym, ext)
+  return if o[sym].nil? or o[sym].empty?
+  r_dir  = MiGA::Dataset.RESULT_DIRS[res_sym]
+  r_path = File.expand_path("data/#{r_dir}/#{d.name}", p.path)
+  ext.each_index do |i|
+    FileUtils.cp o[sym][i], "#{r_path}#{ext[i]}" unless o[sym][i].nil?
+  end
+  File.open("#{r_path}.done", "w") { |f| f.print Time.now.to_s }
+end
+if in_files.any? { |i| not o[i].nil? }
+  $stderr.puts "Copying files." unless o[:q]
+  # :raw_reads
+  cp_result(o, d, p, :raw_reads, :raw_reads, %w[.1.fastq .2.fastq])
+  # :trimmed_fasta
+  cp_result(o, d, p, :trimmed_fasta_s, :trimmed_fasta, %w[.SingleReads.fa])
+  if (o[:trimmed_fasta_c] || []).size > 1
+    cp_result(o, d, p, :trimmed_fasta_c, :trimmed_fasta, %w[.1.fasta .2.fasta])
+  else
+    cp_result(o, d, p, :trimmed_fasta_c, :trimmed_fasta, %w[.CoupledReads.fa])
+  end
+  # :assembly
+  cp_result(o, d, p, :assembly, :assembly, %w[.LargeContigs.fna])
+end
+
 unless o[:metadata].nil?
   o[:metadata].split(",").each do |pair|
     (k,v) = pair.split("=")
     case v
-    when "true"
-      v = true
-    when "false"
-      v = false
-    when "nil"
-      v = nil
+      when "true";  v = true
+      when "false"; v = false
+      when "nil";   v = nil
     end
     d.metadata[k] = v
   end

data/actions/daemon.rb

@@ -32,10 +32,10 @@ OptionParser.new do |opt|
   opt_common(opt, o)
   opt.separator "Daemon options:"
   opt.on("-t", "--ontop",
-    "Stay on top (does not daemonize)"){ o[:daemon_opts] << '-t' }
-  opt.on("-f", "--force", "Force operation"){ o[:daemon_opts] << '-f' }
+    "Stay on top (does not daemonize)."){ o[:daemon_opts] << '-t' }
+  opt.on("-f", "--force", "Force operation."){ o[:daemon_opts] << '-f' }
   opt.on("-n", "--no_wait",
-    "Do not wait for processes to stop"){ o[:daemon_opts] << '-n' }
+    "Do not wait for processes to stop."){ o[:daemon_opts] << '-n' }
   opt.on("--shush", "Silence the daemon."){ o[:daemon_opts] << '--shush' }
 end.parse!
 

data/actions/result_stats.rb

@@ -3,12 +3,17 @@
 # @package MiGA
 # @license Artistic-2.0
 
-o = {q:true}
+o = {q:true, try_load:false}
 opts = OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project, :dataset_opt, :result])
+  opt.on("--key STRING",
+    "Returns only the value of the requested key."){ |v| o[:key] = v }
   opt.on("--compute-and-save",
     "Computes and saves the statistics."){ |v| o[:compute] = v }
+  opt.on("--try-load",
+    "Checks if stat exists instead of computing on --compute-and-save."
+    ){ |v| o[:try_load] = v }
   opt_common(opt, o)
 end.parse!
 
@@ -29,6 +34,9 @@ else
 end
 raise "Cannot load result." if r.nil?
 
+o[:compute] = false if o[:try_load] and
+  (not r[:stats].nil?) and (not r[:stats].empty?)
+
 if o[:compute]
   $stderr.puts "Computing statistics." unless o[:q]
   stats = {}
@@ -78,8 +86,14 @@ if o[:compute]
   end
 end
 
-r[:stats].each do |k,v|
-  puts "#{k.to_s.unmiga_name.capitalize}: #{v.is_a?(Array) ? v.join(" ") : v}."
+if o[:key].nil?
+  r[:stats].each do |k,v|
+    puts "#{k.to_s.unmiga_name.capitalize}: #{
+      v.is_a?(Array) ? v.join(" ") : v}."
+  end
+else
+  v = r[:stats][o[:key].downcase.miga_name.to_sym]
+  puts v.is_a?(Array) ? v.first : v
 end
 
 $stderr.puts "Done." unless o[:q]

data/lib/miga/daemon.rb

@@ -244,7 +244,7 @@ class MiGA::Daemon < MiGA::MiGA
     check_datasets
     check_project
     flush!
-    if loop_i==12
+    if loop_i==4
       say "Housekeeping for sanity"
       @loop_i = 0
       purge!

data/lib/miga/dataset_result.rb

@@ -25,6 +25,7 @@ module MiGA::DatasetResult
         {:pair1=>".1.clipped.fastq", :pair2=>".2.clipped.fastq"}) if
         result_files_exist?(base, ".2.clipped.fastq")
       r.add_file(:single, name + ".1.clipped.single.fastq")
+      r.add_file(:trimming_sumary, name + ".1.fastq.trimmed.summary.txt")
       add_result(:raw_reads) #-> Post gunzip
       r
     end
@@ -60,7 +61,7 @@ module MiGA::DatasetResult
       return nil unless result_files_exist?(base, ".LargeContigs.fna")
       r = MiGA::Result.new(base + ".json")
       r = add_files_to_ds_result(r, name, {:largecontigs=>".LargeContigs.fna",
-        :allcontigs=>".AllContigs.fna"})
+        :allcontigs=>".AllContigs.fna", :assembly_data=>""})
       add_result(:trimmed_fasta) #-> Post interposing
       r
     end

data/lib/miga/project.rb

@@ -2,11 +2,14 @@
 # @license Artistic-2.0
 
 require "miga/dataset"
+require "miga/project_result"
 
 ##
 # MiGA representation of a project.
 class MiGA::Project < MiGA::MiGA
   
+  include MiGA::ProjectResult
+
   # Class-level
 
   ##
@@ -365,62 +368,4 @@ class MiGA::Project < MiGA::MiGA
     plugins.each { |pl| require File.expand_path("lib-plugin.rb", pl) }
   end
 
-  private
-
-    ##
-    # Internal alias for all add_result_*_distances.
-    def add_result_distances(base)
-      return nil unless result_files_exist?(base, %w[.Rdata .log .txt])
-      r = Result.new(base + ".json")
-      r.add_file(:rdata, "miga-project.Rdata")
-      r.add_file(:matrix, "miga-project.txt")
-      r.add_file(:log, "miga-project.log")
-      r.add_file(:hist, "miga-project.hist")
-      r
-    end
-
-    def add_result_clade_finding(base)
-      return nil unless result_files_exist?(base,
-        %w[.proposed-clades])
-      return nil unless is_clade? or result_files_exist?(base,
-        %w[.pdf .classif .medoids .class.tsv .class.nwk])
-      r = add_result_iter_clades(base)
-      r.add_file(:aai_tree,	"miga-project.aai.nwk")
-      r.add_file(:proposal,	"miga-project.proposed-clades")
-      r.add_file(:clades_aai90,	"miga-project.aai90-clades")
-      r.add_file(:clades_ani95,	"miga-project.ani95-clades")
-      r
-    end
-
-    def add_result_subclades(base)
-      return nil unless result_files_exist?(base,
-        %w[.pdf .classif .medoids .class.tsv .class.nwk])
-      r = add_result_iter_clades(base)
-      r.add_file(:ani_tree, "miga-project.ani.nwk")
-      r
-    end
-
-    def add_result_iter_clades(base)
-      r = Result.new(base + ".json")
-      r.add_file(:report,	"miga-project.pdf")
-      r.add_file(:class_table,	"miga-project.class.tsv")
-      r.add_file(:class_tree,	"miga-project.class.nwk")
-      r.add_file(:classif,	"miga-project.classif")
-      r.add_file(:medoids,	"miga-project.medoids")
-      r
-    end
-
-    def add_result_ogs(base)
-      return nil unless result_files_exist?(base, %w[.ogs .stats])
-      r = Result.new(base + ".json")
-      r.add_file(:ogs, "miga-project.ogs")
-      r.add_file(:stats, "miga-project.stats")
-      r.add_file(:rbm, "miga-project.rbm")
-      r
-    end
-
-    alias add_result_haai_distances add_result_distances
-    alias add_result_aai_distances add_result_distances
-    alias add_result_ani_distances add_result_distances
-    alias add_result_ssu_distances add_result_distances
 end

data/lib/miga/project_result.rb

@@ -0,0 +1,67 @@
+# @package MiGA
+# @license Artistic-2.0
+
+##
+# Helper module including specific functions to add project results.
+module MiGA::ProjectResult
+
+  private
+
+    ##
+    # Internal alias for all add_result_*_distances.
+    def add_result_distances(base)
+      return nil unless result_files_exist?(base, %w[.Rdata .log .txt])
+      r = Result.new(base + ".json")
+      r.add_file(:rdata, "miga-project.Rdata")
+      r.add_file(:matrix, "miga-project.txt")
+      r.add_file(:log, "miga-project.log")
+      r.add_file(:hist, "miga-project.hist")
+      r
+    end
+
+    def add_result_clade_finding(base)
+      return nil unless result_files_exist?(base,
+        %w[.proposed-clades])
+      return nil unless is_clade? or result_files_exist?(base,
+        %w[.pdf .classif .medoids .class.tsv .class.nwk])
+      r = add_result_iter_clades(base)
+      r.add_file(:aai_tree,	"miga-project.aai.nwk")
+      r.add_file(:proposal,	"miga-project.proposed-clades")
+      r.add_file(:clades_aai90,	"miga-project.aai90-clades")
+      r.add_file(:clades_ani95,	"miga-project.ani95-clades")
+      r
+    end
+
+    def add_result_subclades(base)
+      return nil unless result_files_exist?(base,
+        %w[.pdf .classif .medoids .class.tsv .class.nwk])
+      r = add_result_iter_clades(base)
+      r.add_file(:ani_tree, "miga-project.ani.nwk")
+      r
+    end
+
+    def add_result_iter_clades(base)
+      r = Result.new(base + ".json")
+      r.add_file(:report,	"miga-project.pdf")
+      r.add_file(:class_table,	"miga-project.class.tsv")
+      r.add_file(:class_tree,	"miga-project.class.nwk")
+      r.add_file(:classif,	"miga-project.classif")
+      r.add_file(:medoids,	"miga-project.medoids")
+      r
+    end
+
+    def add_result_ogs(base)
+      return nil unless result_files_exist?(base, %w[.ogs .stats])
+      r = Result.new(base + ".json")
+      r.add_file(:ogs, "miga-project.ogs")
+      r.add_file(:stats, "miga-project.stats")
+      r.add_file(:rbm, "miga-project.rbm")
+      r
+    end
+
+    alias add_result_haai_distances add_result_distances
+    alias add_result_aai_distances add_result_distances
+    alias add_result_ani_distances add_result_distances
+    alias add_result_ssu_distances add_result_distances
+
+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 = [0.2, 2, 2]
+  VERSION = [0.2, 3, 0]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2016, 8, 31)
+  VERSION_DATE = Date.new(2017, 3, 14)
   
   ##
   # Reference of MiGA.

data/scripts/_distances_functions.bash

@@ -16,11 +16,11 @@ fi
 fx_exists miga-make_empty_aai_db || function miga-make_empty_aai_db {
   local DB=$1
   echo "create table if not exists aai(seq1 varchar(256), seq2 varchar(256)," \
-    " aai float, sd float, n int, omega int);" | sqlite3 $DB
+    " aai float, sd float, n int, omega int);" | sqlite3 "$DB"
 }
 
 fx_exists miga-ds_name || function miga-ds_name {
-  basename $1 | perl -pe "s/[^A-Za-z0-9_].*//"
+  basename "$1" | perl -pe "s/[^A-Za-z0-9_].*//"
 }
 
 fx_exists miga-aai || function miga-aai {
@@ -28,10 +28,10 @@ fx_exists miga-aai || function miga-aai {
   local F2=$2
   local TH=$3
   local DB=$4
-  local N1=$(miga-ds_name $F1)
-  local N2=$(miga-ds_name $F2)
-  aai.rb -1 $F1 -2 $F2 -t $TH -a --lookup-first -S $DB --name1 $N1 --name2 $N2 \
-    --$MIGA_AAI_SAVE_RBM || echo "0"
+  local N1=$(miga-ds_name "$F1")
+  local N2=$(miga-ds_name "$F2")
+  aai.rb -1 "$F1" -2 "$F2" -t "$TH" -a --lookup-first -S "$DB" --name1 "$N1" \
+    --name2 "$N2" --$MIGA_AAI_SAVE_RBM || echo "0"
 }
 
 fx_exists miga-ani || function miga-ani {
@@ -39,10 +39,10 @@ fx_exists miga-ani || function miga-ani {
   local F2=$2
   local TH=$3
   local DB=$4
-  local N1=$(miga-ds_name $F1)
-  local N2=$(miga-ds_name $F2)
-  ani.rb -1 $F1 -2 $F2 -t $TH -a --no-save-regions --no-save-rbm \
-    --lookup-first -S $DB --name1 $N1 --name2 $N2 || echo "0"
+  local N1=$(miga-ds_name "$F1")
+  local N2=$(miga-ds_name "$F2")
+  ani.rb -1 "$F1" -2 "$F2" -t "$TH" -a --no-save-regions --no-save-rbm \
+    --lookup-first -S "$DB" --name1 "$N1" --name2 "$N2" || echo "0"
 }
 
 fx_exists miga-haai || function miga-haai {
@@ -51,14 +51,14 @@ fx_exists miga-haai || function miga-haai {
   local TH=$3
   local DB=$4
   local AAI_DB=$5
-  local N1=$(miga-ds_name $F1)
-  local N2=$(miga-ds_name $F2)
-  local HAAI=$(MIGA_AAI_SAVE_RBM="no-save-rbm" miga-aai $F1 $F2 $TH $DB)
+  local N1=$(miga-ds_name "$F1")
+  local N2=$(miga-ds_name "$F2")
+  local HAAI=$(MIGA_AAI_SAVE_RBM="no-save-rbm" miga-aai "$F1" "$F2" "$TH" "$DB")
   if [[ "$HAAI" != "" && $(perl -e "print 1 if '$HAAI' <= 90") == "1" ]] ; then
     local AAI=$(perl -e "print (100-exp(2.435076 + 0.4275193*log(100-$HAAI)))")
-    [[ ! -s $AAI_DB ]] && make_empty_aai_db $AAI_DB
-    echo "insert into aai values('$N1','$N2','$AAI',0,0,0);" | sqlite3 $AAI_DB
-    echo $AAI
+    [[ ! -s $AAI_DB ]] && make_empty_aai_db "$AAI_DB"
+    echo "insert into aai values('$N1','$N2','$AAI',0,0,0);" | sqlite3 "$AAI_DB"
+    echo "$AAI"
   fi
 }
 
@@ -70,9 +70,9 @@ fx_exists miga-haai_or_aai || function miga-haai_or_aai {
   local  F2=$5
   local  DB=$6
   local  TH=$7
-  AAI=$(miga-haai $FH1 $FH2 $TH $DBH $DB)
-  [[ "${AAI%.*}" -le 0 ]] && AAI=$(miga-aai $F1 $F2 $TH $DB)
-  echo $AAI
+  AAI=$(miga-haai "$FH1" "$FH2" "$TH" "$DBH" "$DB")
+  [[ "${AAI%.*}" -le 0 ]] && AAI=$(miga-aai "$F1" "$F2" "$TH" "$DB")
+  echo "$AAI"
 }
 
 fx_exists miga-val_from_db || function miga-val_from_db {
@@ -82,14 +82,14 @@ fx_exists miga-val_from_db || function miga-val_from_db {
   local MT=$4
   if [[ -s $DB ]] ; then
     echo "select $MT from $MT where seq1='$N1' and seq2='$N2';" \
-      | sqlite3 $DB || echo 0
+      | sqlite3 "$DB" || echo 0
   fi
 }
 
 fx_exists miga-aai_from_db || function miga-aai_from_db {
-  miga-val_from_db $1 $2 $3 aai
+  miga-val_from_db "$1" "$2" "$3" aai
 }
 
 fx_exists miga-ani_from_db || function miga-ani_from_db {
-  miga-val_from_db $1 $2 $3 ani
+  miga-val_from_db "$1" "$2" "$3" ani
 }

data/scripts/_distances_noref_nomulti.bash

@@ -5,9 +5,9 @@
 set -e
 
 # Deal with previous runs (if any)
-exists $DATASET.haai.db && cp $DATASET.haai.db $TMPDIR
-exists $DATASET.a[an]i.db && cp $DATASET.a[an]i.db $TMPDIR
-exists $DATASET.a[an]i.9[05] && rm $DATASET.a[an]i.9[05]
+exists "$DATASET".haai.db && cp "$DATASET".haai.db "$TMPDIR"
+exists "$DATASET".a[an]i.db && cp "$DATASET".a[an]i.db "$TMPDIR"
+exists "$DATASET".a[an]i.9[05] && rm "$DATASET".a[an]i.9[05]
 N=0
 fx_exists miga-checkpoint_n || function miga-checkpoint_n {
   let N=$N+1
@@ -15,9 +15,9 @@ fx_exists miga-checkpoint_n || function miga-checkpoint_n {
     for metric in haai aai ani ; do
       if [[ -s $TMPDIR/$DATASET.$metric.db ]] ; then
         echo "select count(*) from ${metric#h};" \
-          | sqlite3 $TMPDIR/$DATASET.$metric.db \
+          | sqlite3 "$TMPDIR/$DATASET.$metric.db" \
           >/dev/null || exit 1
-        cp $TMPDIR/$DATASET.$metric.db .
+        cp "$TMPDIR/$DATASET.$metric.db" .
       fi
     done
     N=0
@@ -28,18 +28,18 @@ fx_exists miga-noref_haai_or_aai || function miga-noref_haai_or_aai {
   local Q=$1
   local S=$2
   [[ -s $TMPDIR/$Q.faa ]] \
-    || cp ../06.cds/$Q.faa $TMPDIR/$Q.faa
-  miga-haai_or_aai $ESS/$Q.ess.faa $ESS/$S.ess.faa $TMPDIR/$Q.haai.db \
-    $TMPDIR/$Q.faa ../06.cds/$S.faa $TMPDIR/$Q.aai.db $CORES
+    || cp "../06.cds/$Q.faa" "$TMPDIR/$Q.faa"
+  miga-haai_or_aai "$ESS/$Q.ess.faa" "$ESS/$S.ess.faa" "$TMPDIR/$Q.haai.db" \
+    "$TMPDIR/$Q.faa" "../06.cds/$S.faa" "$TMPDIR/$Q.aai.db" "$CORES"
 }
 
 fx_exists miga-noref_ani || function miga-noref_ani {
   local Q=$1
   local S=$2
   [[ -s $TMPDIR/$Q.LargeContigs.fna ]] \
-    || cp ../05.assembly/$Q.LargeContigs.fna $TMPDIR/$Q.LargeContigs.fna
-  miga-ani $TMPDIR/$Q.LargeContigs.fna ../05.assembly/$S.LargeContigs.fna \
-    $CORES $TMPDIR/$Q.ani.db
+    || cp ../05.assembly/$Q.LargeContigs.fna "$TMPDIR/$Q.LargeContigs.fna"
+  miga-ani "$TMPDIR/$Q.LargeContigs.fna" "../05.assembly/$S.LargeContigs.fna" \
+    "$CORES" "$TMPDIR/$Q.ani.db"
 }
 
 
@@ -63,12 +63,12 @@ while [[ -e "$CLADES/$CLASSIF/miga-project.medoids" ]] ; do
   VAL_MED=""
   VAL_CLS=""
   i_n=0
-  for i in $(cat "$CLADES/$CLASSIF/miga-project.medoids") ; do
+  while read i ; do
     let i_n=$i_n+1
     if [[ $METRIC == "aai" ]] ; then
-      VAL=$(miga-noref_haai_or_aai $DATASET $i)
+      VAL=$(miga-noref_haai_or_aai "$DATASET" "$i")
     else
-      VAL=$(miga-noref_ani $DATASET $i)
+      VAL=$(miga-noref_ani "$DATASET" "$i")
     fi
     miga-checkpoint_n
     if [[ $(perl -e "print 1 if '$VAL' >= '$MAX_VAL'") == "1" ]] ; then
@@ -77,7 +77,7 @@ while [[ -e "$CLADES/$CLASSIF/miga-project.medoids" ]] ; do
       VAL_CLS=$i_n
       echo "[$CLASSIF] New max: $VAL_MED ($VAL_CLS): $MAX_VAL"
     fi
-  done
+  done < "$CLADES/$CLASSIF/miga-project.medoids"
   CLASSIF="$CLASSIF/miga-project.sc-$VAL_CLS"
   echo "$VAL_CLS	$VAL_MED	$MAX_VAL	$CLASSIF" \
     >> "$DATASET.$METRIC-medoids.tsv"
@@ -87,17 +87,17 @@ done
 if [[ "$CLASSIF" != "." ]] ; then
   PAR=$(dirname "$CLADES/$CLASSIF")/miga-project.classif
   if [[ -s "$PAR" ]] ; then
-    for i in $(cat "$PAR" | awk "\$2==$VAL_CLS{print \$1}") ; do
+    while read i ; do
       if [[ $METRIC == "aai" ]] ; then
-        AAI=$(miga-noref_haai_or_aai $DATASET $i)
+        AAI=$(miga-noref_haai_or_aai "$DATASET" "$i")
       else
         AAI=100
       fi
       if [[ $(perl -e "print 1 if '$AAI' >= 90") == "1" ]] ; then
-        miga-noref_ani $DATASET $i
+        miga-noref_ani "$DATASET" "$i"
       fi
       miga-checkpoint_n
-    done
+    done < <(awk "\$2==$VAL_CLS{print \$1}" < "$PAR")
   fi
 fi
 

data/scripts/_distances_ref_nomulti.bash

@@ -11,9 +11,9 @@ fx_exists miga-checkpoint_n || function miga-checkpoint_n {
         tab="aai"
         [[ "$t" == "03.ani" ]] && tab="ani"
         echo "select count(*) from $tab;" \
-          | sqlite3 $TMPDIR/$t.db \
+          | sqlite3 "$TMPDIR/$t.db" \
           >/dev/null || exit 1
-        cp $TMPDIR/$t.db $t/$DATASET.db
+        cp "$TMPDIR/$t.db" "$t/$DATASET.db"
       fi
     done
     N=0
@@ -25,7 +25,7 @@ ESS="../07.annotation/01.function/01.essential"
 
 # Initialize temporals
 for t in 01.haai 02.aai 03.ani ; do
-  [[ -s $t/$DATASET.db ]] && cp $t/$DATASET.db $TMPDIR/$t.db
+  [[ -s $t/$DATASET.db ]] && cp "$t/$DATASET.db" "$TMPDIR/$t.db"
 done
 N=1
 
@@ -36,38 +36,40 @@ for i in $(miga list_datasets -P "$PROJECT" --ref --no-multi) ; do
   # Check if the i-th dataset is ready
   [[ -s $ESS/$i.done && -s $ESS/$i.json ]] || continue
   # Check if this is done (e.g., in a previous failed iteration)
-  AAI=$(miga-aai_from_db $DATASET $i $TMPDIR/02.aai.db)
+  AAI=$(miga-aai_from_db "$DATASET" "$i" "$TMPDIR/02.aai.db")
   # Try the other direction
-  [[ "${AAI%.*}" -le 0 ]] && AAI=$(miga-aai_from_db $i $DATASET 02.aai/$i.db)
+  [[ "${AAI%.*}" -le 0 ]] \
+    && AAI=$(miga-aai_from_db "$i" "$DATASET" "02.aai/$i.db")
   # Try with hAAI
   if [[ "${AAI%.*}" -le 0 ]] ; then
     [[ -e "$TMPDIR/$DATASET.ess.faa" ]] \
-      || cp $ESS/$DATASET.ess.faa $TMPDIR/$DATASET.ess.faa
-    AAI=$(miga-haai $TMPDIR/$DATASET.ess.faa $ESS/$i.ess.faa \
-      $CORES $TMPDIR/01.haai.db $TMPDIR/02.aai.db)
+      || cp "$ESS/$DATASET.ess.faa" "$TMPDIR/$DATASET.ess.faa"
+    AAI=$(miga-haai "$TMPDIR/$DATASET.ess.faa" "$ESS/$i.ess.faa" \
+      "$CORES" "$TMPDIR/01.haai.db" "$TMPDIR/02.aai.db")
   fi
   # Try with complete AAI
   if [[ "${AAI%.*}" -le 0 ]] ; then
     [[ -e "$TMPDIR/$DATASET.faa" ]] \
-      || cp ../06.cds/$DATASET.faa $TMPDIR/$DATASET.faa
-    AAI=$(miga-aai $TMPDIR/$DATASET.faa ../06.cds/$i.faa \
-      $CORES $TMPDIR/02.aai.db)
+      || cp "../06.cds/$DATASET.faa" "$TMPDIR/$DATASET.faa"
+    AAI=$(miga-aai "$TMPDIR/$DATASET.faa" "../06.cds/$i.faa" \
+      "$CORES" "$TMPDIR/02.aai.db")
   fi
   # Check if ANI is meaningful
   if [[ -e "../05.assembly/$DATASET.LargeContigs.fna" \
       && -e "../05.assembly/$i.LargeContigs.fna" \
       && $(perl -e "print 1 if '$AAI' >= 90") == "1" ]] ; then
     # Check if this is done (e.g., in a previous failed iteration)
-    ANI=$(miga-ani_from_db $DATASET $i $TMPDIR/03.ani.db)
+    ANI=$(miga-ani_from_db "$DATASET" "$i" "$TMPDIR/03.ani.db")
     # Try the other direction
-    [[ "${ANI%.*}" -le 0 ]] && ANI=$(miga-ani_from_db $i $DATASET 03.ani/$i.db)
+    [[ "${ANI%.*}" -le 0 ]] \
+      && ANI=$(miga-ani_from_db "$i" "$DATASET" "03.ani/$i.db")
     # Calculate it
     if [[ "${ANI%.*}" -le 0 ]] ; then
       [[ -e "$TMPDIR/$DATASET.LargeContigs.fna" ]] \
-        || cp ../05.assembly/$DATASET.LargeContigs.fna \
-          $TMPDIR/$DATASET.LargeContigs.fna
-      ANI=$(miga-ani $TMPDIR/$DATASET.LargeContigs.fna \
-        ../05.assembly/$i.LargeContigs.fna $CORES $TMPDIR/03.ani.db)
+        || cp "../05.assembly/$DATASET.LargeContigs.fna" \
+          "$TMPDIR/$DATASET.LargeContigs.fna"
+      ANI=$(miga-ani "$TMPDIR/$DATASET.LargeContigs.fna" \
+        "../05.assembly/$i.LargeContigs.fna" "$CORES" "$TMPDIR/03.ani.db")
     fi
   fi
   miga-checkpoint_n

data/test/daemon_test.rb

@@ -57,8 +57,8 @@ class DaemonTest < Test::Unit::TestCase
     end
     assert_equal(DateTime, d.last_alive.class)
     assert(out.string =~ /-{20}\n.*MiGA:#{p.name} launched/)
-    10.times{ d.in_loop }
-    assert_equal(11, d.loop_i)
+    2.times{ d.in_loop }
+    assert_equal(3, d.loop_i)
     out = capture_stdout do
       d.in_loop
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.2.2.2
+  version: 0.2.3.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-08-31 00:00:00.000000000 Z
+date: 2017-03-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -94,6 +94,7 @@ files:
 - lib/miga/dataset_result.rb
 - lib/miga/metadata.rb
 - lib/miga/project.rb
+- lib/miga/project_result.rb
 - lib/miga/remote_dataset.rb
 - lib/miga/result.rb
 - lib/miga/tax_dist.rb
@@ -191,8 +192,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.14
+rubygems_version: 2.0.14.1
 signing_key: 
 specification_version: 4
 summary: MiGA
 test_files: []
+has_rdoc: true