sequenceserver 1.0.0.pre.4 → 1.0.0.pre.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 9ed1609668685537118f3ff44bb18bda69cbdf8b
-  data.tar.gz: d2b5aa23928abb0ed230747e789b45440b9927fa
+  metadata.gz: e3a82c074774e6df93a1a55e2261c8267cf60048
+  data.tar.gz: 9d5fb2432833c4dc25e472b14fd93200f03f8fe7
 SHA512:
-  metadata.gz: a2b7d392d183377a918b4841685adc34fe26997b73eda7f5129273064bf8bae30929448ea8fd4818508728957460cc20c299b375ba644405060ccbed432ac5fa
-  data.tar.gz: bdca19b354e1b70113d2c77fc99699c4150e30e61e8fe5a82195d8e8033ad826a82ea7fdd9fde69a0528197d4aa739648f2bfd0d31f81d2da25dd7b32e520bfc
+  metadata.gz: a4334e199b5dd02c67bdac5352918b840f3c39911583132601682aec5ca215f365f06d9f67494692c258c9075db3a9217fd91b6fa8baa50c5795f8e25bd6071b
+  data.tar.gz: 10e137003e87a4e0aee3c83183dd88dc65948f313186b100188ea0a50b4c644f49b8894ee07ecc53e9161d5eebc28e943b6545c136fc4059a52ccede2fd4fcc0

data/bin/sequenceserver

@@ -305,7 +305,7 @@ MSG
           puts e
 
           # Offer user to format the FASTA files.
-          database_dir = SequenceServer[:database_dir]
+          database_dir = SequenceServer.config[:database_dir]
           puts
           puts <<MSG
 Search for FASTA files (.fa, .fasta, .fna) in '#{database_dir}' and try
@@ -344,8 +344,8 @@ MSG
       if list_unformatted_fastas? || make_blast_databases?
         unformatted_fastas = SequenceServer::Database.unformatted_fastas
         if unformatted_fastas.empty?
-          puts "All FASTA files in #{SequenceServer[:database_dir]} are "\
-               'formatted.'
+          puts "All FASTA files in #{SequenceServer.config[:database_dir]} " \
+               'are formatted.'
           exit
         end
       end

data/lib/sequenceserver/blast/constants.rb

@@ -11,7 +11,7 @@ module SequenceServer
                            mismatch positive gapopen gaps ppos frames
                            qframe hframe btop staxids sscinames scomnames
                            sblastnames sskingdoms stitle salltitles sstrand
-                           qcovs qcovhsp)
+                           qcovs qcovhsp).join(' ')
     OUTFMT = {
       'pairwise'        => [0, :txt],
       'qa'              => [1, :txt],

data/lib/sequenceserver/blast/hit.rb

@@ -26,7 +26,7 @@ module SequenceServer
       def links
         links = Links.instance_methods.map { |m| send m }
         links.compact!
-        links.sort_by! { |link| link[:order] }
+        links.sort_by { |link| link[:order] }
       end
 
       # Returns an array of database objects which contain the queried sequence

data/lib/sequenceserver/database.rb

@@ -203,7 +203,7 @@ module SequenceServer
         # replaces _ with ' ',
         db_name.gsub!(/(_)/, ' ')
         # replaces '.' with ' ' when no numbers are on either side,
-        db_name.gsub!(/(?<![0-9])\.(?![0-9])/, ' ')
+        db_name.gsub!(/(\D)\.(?=\D)/, '\1 ')
         # preserves version numbers
         db_name.gsub!(/\W*(\d+([.-]\d+)+)\W*/, ' \1 ')
         db_name

data/lib/sequenceserver/sequence.rb

@@ -192,9 +192,10 @@ module SequenceServer
 
         logger.debug("Executing: #{command}")
 
-        @sequences = `#{command} 2> /dev/null`.each_line
-                     .map { |line| Sequence.new(*line.chomp.split('	')) }
-
+        out = `#{command} 2> /dev/null`
+        @sequences = out.each_line.map do |line|
+          Sequence.new(*line.chomp.split('	'))
+        end
         extend(IO) && write if in_file
       end
 

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '1.0.0-4'
+  s.version     = '1.0.0-5'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft',
                    'Vivek Rai', 'Yannick Wurm']
   s.email       = ['anurag08priyam@gmail.com', 'b.woodcroft@uq.edu.au']
@@ -17,6 +17,7 @@ DESC
   # dependencies
   s.add_dependency('thin',    '~> 1.6',  '>= 1.6.2')
   s.add_dependency('sinatra', '~> 1.4',  '>= 1.4.5')
+  s.add_dependency('json',    '~> 1.8',  '>= 1.8.2')
   s.add_dependency('ox',      '~> 2.1',  '>= 2.1.1')
   s.add_dependency('slop',    '~> 3.6',  '>= 3.6.0')
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 1.0.0.pre.4
+  version: 1.0.0.pre.5
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-20 00:00:00.000000000 Z
+date: 2015-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: thin
@@ -53,6 +53,26 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.5
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.8.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.8.2
 - !ruby/object:Gem::Dependency
   name: ox
   requirement: !ruby/object:Gem::Requirement