miga-base 1.4.2.1 → 1.4.2.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 2eb3548ca6e3ab2dbd8e4cffee3a72f12c3e1f51f54798633c18a7829812acc4
-  data.tar.gz: 4dff34634631b786c647229977eb994e6a94071dc2a6d043a62e4239ed921ca4
+  metadata.gz: 725b5f62ffeba49a813504c3cfaf5a222ba5259f82eb2cb0430150483e83cc83
+  data.tar.gz: 5c3d9e21668edeb12d022a193a045ec43749c2704484976fa08bcb248cdf8fed
 SHA512:
-  metadata.gz: 55fd0a15cdf186a9a7643912330bf69242856e03713ddaebc7d3e18404d50cf7bba8e78da42c2263449409627d8e153aa2050cdb014439162dc57e0cc04e6d58
-  data.tar.gz: 87bc8bd8b7b990f0c686c2deea27a34af79f32f95a15eb3dd0e6d3561ab32ea72c4eea87a847854135178a0d39f4f57d60cfb561031ba1e873dc7f134c9a3f0b
+  metadata.gz: c9746ea4048074e5478c087f81293bd0ee64da5a9e4c51b86d4a62d1c76f0de43a92a8a539349df8b8e0adb5fe8ad58f6594d523ce7858bcc861f265dc62c7d6
+  data.tar.gz: 276f2aabeb61253b8d2a6d219517c9334f9ac63317b0daa4482af474ed9106adc667458214619f1245cdc9c1b88627dd6440b5369c1752bfbc5e63cba6e474b8

data/Gemfile

@@ -7,3 +7,5 @@ group :test do
 end
 
 gem 'rake', '~> 13.0'
+
+gem "csv", "~> 3.3"

data/lib/miga/cli/action/init/files_helper.rb

@@ -64,12 +64,33 @@ module MiGA::Cli::Action::Init::FilesHelper
 
   def check_mytaxa_scores(paths)
     cli.print 'Looking for MyTaxa scores... '
-    mt = File.dirname(paths['MyTaxa'])
-    unless Dir.exist?(File.join(mt, 'db'))
-      cli.puts "no\nExecute 'python2 #{mt}/utils/download_db.py'"
-      raise 'Incomplete MyTaxa installation'
+    arch    = 'mytaxa_db.tar.gz'
+    mt      = File.dirname(paths['MyTaxa'])
+    mt_db   = File.join(mt, 'db')
+    mt_db_1 = File.join(mt_db, 'ncbiSciNames.lib')
+    miga_db = File.join(ENV['MIGA_HOME'], '.miga_db', 'mytaxa')
+    home_db = File.join(miga_db, 'db')
+    home_db_1 = File.join(home_db, 'ncbiSciNames.lib')
+
+    if File.exist?(home_db_1)
+      cli.puts 'yes'
+    elsif File.exist?(mt_db_1)
+      cli.puts 'yes, sym-linking'
+      FileUtils.mkdir_p(miga_db)
+      File.symlink(mt_db, home_db)
+    else
+      cli.puts 'no, downloading'
+      MiGA::MiGA.download_file_ftp(
+        :miga_dist, arch, File.join(miga_db, arch)
+      ) { |n, size| cli.advance("#{arch}:", n, size) }
+      cmd = <<~CMD
+        cd #{miga_db.shellescape} \
+          && tar zxf #{arch.shellescape} \
+          && rm #{arch.shellescape}
+      CMD
+      run_cmd(cli, cmd, source: nil)
+      cli.puts
     end
-    cli.puts 'yes'
   end
 
   def check_mytaxa_database(paths)

data/lib/miga/common/format.rb

@@ -24,10 +24,11 @@ module MiGA::Common::Format
 
   ##
   # Cleans a FastA file in place, removing all sequences shorter than
-  # +min_len+
+  # +min_len+ and renaming duplicate sequence identifiers
   def clean_fasta_file(file, min_len = 1)
     tmp_fh = nil
     tmp_path = nil
+    names = Set.new
     begin
       if file =~ /\.gz/
         tmp_path = Tempfile.new('MiGA.gz').tap(&:close).path
@@ -45,11 +46,14 @@ module MiGA::Common::Format
         ln.chomp!
         if ln =~ /^>\s*(\S+)(.*)/
           id, df = $1, $2
+          id = id.gsub(/[^A-Za-z0-9_\|\.]/, '_')
+          id = id + '_dup' while names.include?(id)
+          names << id
           if next_seq[1].length >= min_len
             tmp_fh.puts next_seq[0]
             tmp_fh.print next_seq[1].wrap_width(80)
           end
-          next_seq = [">#{id.gsub(/[^A-Za-z0-9_\|\.]/, '_')}#{df}", '']
+          next_seq = [">#{id}#{df}", '']
         else
           next_seq[1] += ln.gsub(/[^A-Za-z]/, '')
         end

data/lib/miga/common/net.rb

@@ -118,7 +118,7 @@ module MiGA::Common::Net
   def http_request(method, url, *opts)
     doc = nil
     remote_connection(url).start do |http|
-      res = http.send(method, remote_connection_uri.to_s, *opts)
+      res = http.send(method, remote_connection_uri, *opts)
       if %w[301 302].include?(res.code)
         DEBUG "REDIRECTION #{res.code}: #{res['location']}"
         return http_request(method, res['location'], *opts)

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 = [1.4, 2, 1].freeze
+  VERSION = [1.4, 2, 5].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2026, 3, 19)
+  VERSION_DATE = Date.new(2026, 5, 20)
 
   ##
   # References of MiGA

data/scripts/mytaxa.bash

@@ -27,12 +27,21 @@ else
             "no such file or directory" >&2
       exit 1
     fi
-    if [[ ! -d "$MT/db" && ! -d "$MYTAXA_DB" ]] ; then
-      echo "Cannot locate the MyTaxa index: $MT/db" >&2
-      exit 1
+    if [[ -d "$MYTAXA_DB" ]] ; then
+      echo "Using MYTAXA_DB=$MYTAXA_DB"
+    elif [[ -d "$MIGA_HOME/.miga_db/mytaxa/db" ]] ; then
+      export MYTAXA_DB="$MIGA_HOME/.miga_db/mytaxa/db"
+    elif [[ -d "$MT/db" ]] ; then
+      export MYTAXA_DB="$MT/db"
+    else
+     echo "Cannot locate the MyTaxa scores: rerun 'miga init'" >&2 
+     exit 1
     fi
-    if [[ ! -d "$MT/utils" ]] ; then
-      echo "Cannot locate the MyTaxa utilities: $MT/utils" >&2
+    MT_UTILS="$MT/utils"
+    [[ -n "$CONDA_PREFIX" && ! -d "$MT_UTILS" ]] \
+      && MT_UTILS="$CONDA_PREFIX/share/mytaxa/utils"
+    if [[ ! -d "$MT_UTILS" ]] ; then
+      echo "Cannot locate the MyTaxa utilities: $MT_UTILS" >&2
       exit 1
     fi
      
@@ -52,30 +61,30 @@ else
       && gunzip "../../../06.cds/$DATASET.gff3.gz"
     if [[ -e "../../../06.cds/$DATASET.gff2" ]] ; then
       # GFF2
-      perl "$MT/utils/infile_convert.pl" -f gff2 \
+      perl "$MT_UTILS/infile_convert.pl" -f gff2 \
         "../../../06.cds/$DATASET.gff2" "$DATASET.blast" \
         | sort -k 13 > "$DATASET.mytaxain"
       "$MT/MyTaxa" "$DATASET.mytaxain" "$DATASET.mytaxa" "0.5"
-      perl "$MT/utils/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
+      perl "$MT_UTILS/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
         -g "../../../06.cds/$DATASET.gff2" -f gff2 \
         -I "$DATASET.mytaxa.innominate" -G "$DATASET.mytaxa.genes" \
         -K "$DATASET.mytaxa.krona" -u
     elif [[ -e "../../../06.cds/$DATASET.gff3" ]] ; then
       # GFF3
-      perl "$MT/utils/infile_convert.pl" -f gff3 \
+      perl "$MT_UTILS/infile_convert.pl" -f gff3 \
         "../../../06.cds/$DATASET.gff3" "$DATASET.blast" | sort -k 13 \
         > "$DATASET.mytaxain"
       "$MT/MyTaxa" "$DATASET.mytaxain" "$DATASET.mytaxa" "0.5"
-      perl "$MT/utils/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
+      perl "$MT_UTILS/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
         -g "../../../06.cds/$DATASET.gff3" -f gff3 \
         -I "$DATASET.mytaxa.innominate" -G "$DATASET.mytaxa.genes" \
         -K "$DATASET.mytaxa.krona" -u
     else
       # No GFF
-      perl "$MT/utils/infile_convert.pl" -f no "LOREM_IPSUM" "$DATASET.blast" \
+      perl "$MT_UTILS/infile_convert.pl" -f no "LOREM_IPSUM" "$DATASET.blast" \
         | sort -k 13 > "$DATASET.mytaxain"
       "$MT/MyTaxa" "$DATASET.mytaxain" "$DATASET.mytaxa" "0.5"
-      perl "$MT/utils/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
+      perl "$MT_UTILS/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
         -I "$DATASET.mytaxa.innominate" -G "$DATASET.mytaxa.genes" \
         -K "$DATASET.mytaxa.krona" -u
     fi

data/scripts/mytaxa_scan.bash

@@ -26,12 +26,21 @@ else
             "no such file or directory" >&2
       exit 1
     fi
-    if [[ ! -d "$MT/db" && ! -d "$MYTAXA_DB" ]] ; then
-      echo "Cannot locate the MyTaxa index: $MT/db" >&2
-      exit 1
+    if [[ -d "$MYTAXA_DB" ]] ; then
+      echo "Using MYTAXA_DB=$MYTAXA_DB"
+    elif [[ -d "$MIGA_HOME/.miga_db/mytaxa/db" ]] ; then
+      export MYTAXA_DB="$MIGA_HOME/.miga_db/mytaxa/db"
+    elif [[ -d "$MT/db" ]] ; then
+      export MYTAXA_DB="$MT/db"
+    else
+     echo "Cannot locate the MyTaxa scores: rerun 'miga init'" >&2 
+     exit 1
     fi
-    if [[ ! -d "$MT/utils" ]] ; then
-      echo "Cannot locate the MyTaxa utilities: $MT/utils" >&2
+    MT_UTILS="$MT/utils"
+    [[ -n "$CONDA_PREFIX" && ! -d "$MT_UTILS" ]] \
+      && MT_UTILS="$CONDA_PREFIX/share/mytaxa/utils"
+    if [[ ! -d "$MT_UTILS" ]] ; then
+      echo "Cannot locate the MyTaxa utilities: $MT_UTILS" >&2
       exit 1
     fi
      
@@ -49,7 +58,7 @@ else
       fi
 
       # Prepare MyTaxa input, execute MyTaxa, and generate profiles
-      perl "$MT/utils/infile_convert.pl" -f no "LOREM_IPSUM" "$DATASET.blast" \
+      perl "$MT_UTILS/infile_convert.pl" -f no "LOREM_IPSUM" "$DATASET.blast" \
         | sort -k 13 > "$DATASET.mytaxain"
       "$MT/MyTaxa" "$DATASET.mytaxain" "$DATASET.mytaxa" "0.5"
     fi

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.4.2.1
+  version: 1.4.2.5
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-03-19 00:00:00.000000000 Z
+date: 2026-05-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons