bio-velvet 0.2.0 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -4,6 +4,7 @@ gem 'bio-logger', '~>1.0'
 gem 'systemu', '~>2.6'
 gem 'files', '~>0.3'
 gem 'hopcsv', '~> 0.4'
+gem 'bio-commandeer', '~>0.1'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
@@ -13,4 +14,5 @@ group :development do
   gem "bundler", "~> 1.0"
   gem "bio", "~> 1.4"
   gem "rdoc", "~> 4.1"
+  gem 'pry', '~>0.9'
 end

data/README.md

@@ -51,6 +51,30 @@ graph.nodes[5].noded_reads #=> array of Bio::Velvet::Graph::NodedRead objects, f
 ```
 There is much more that can be done to interact with the graph object and its components - see the [rubydoc](http://rubydoc.info/gems/bio-velvet/Bio/Velvet/Graph).
 
+### Parsers for `Sequences` and `CnyUnifiedSeq.names` files
+With default parameters velvet generates a `Seqeunces` file, that includes read ID information and the sequences themselves.
+```ruby
+seqs = Bio::Velvet::Sequences.parse_from_file(File.join velvet_result.result_directory, 'Sequences')
+seqs[1] => 'AAAATTGTCAGACTAGCTATCAGCATATCAGCGCGCATCTCAGACGAGCACTATC'
+```
+If the `-create_binary` flag is set when running `velveth`, a names file is generated that encodes the read names and IDs.
+```ruby
+entries = Bio::Velvet::CnyUnifiedSeqNamesFile.extract_entries(
+  File.join(velvet_result.result_directory, 'CnyUnifiedSeq.names'),
+  ['read1','read2']
+  ) #=> Hash of read name to Array of CnyUnifiedSeqNamesFileEntry objects
+entries['read1'] #=> Array of CnyUnifiedSeqNamesFileEntry objects
+entries['read1'][0].read_id #=> 1 (i.e. '1'.to_i)
+```
+When speed is required, grep can come to the rescue (at the cost of some portability)
+```ruby
+entries = Bio::Velvet::CnyUnifiedSeqNamesFile.extract_entries_using_grep_hack(
+  File.join(velvet_result.result_directory, 'CnyUnifiedSeq.names'),
+  ['read1','read2']
+  ) #=> same returned object as above
+```
+The sequences themselves are stored in a separate file when `-create_binary` is used - an interface for this is included in the [bio-velvet_underground](https://github.com/wwood/bioruby-velvet_underground) biogem.
+
 ## Project home page
 
 Information on the source tree, documentation, examples, issues and

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.3.0

data/lib/bio-velvet.rb

@@ -12,3 +12,4 @@ end
 require 'bio-velvet/graph'
 require 'bio-velvet/runner'
 require 'bio-velvet/sequences'
+require 'bio-velvet/sequence_names'

data/lib/bio-velvet/graph.rb

@@ -1,4 +1,4 @@
-require 'hopcsv'
+#require 'hopcsv'
 require 'bio'
 require 'tempfile'
 
@@ -30,6 +30,7 @@ module Bio
       # into a Bio::Velvet::Graph object
       #
       # Options:
+      # * :dont_parse_noded_reads: if true, then parsing of the NR section is skipped
       # * :interesting_read_ids: If not nil, is a Set of nodes that we are interested in. Reads
       # not of interest will not be parsed in (the NR part of the velvet LastGraph file). Regardless all
       # nodes and edges are parsed in. Using this options saves both memory and CPU.
@@ -130,6 +131,7 @@ module Bio
             # $READ_ID2 etc.
             #p row
             if row[0] == 'NR'
+              break if options[:dont_parse_noded_reads] # We are done if NR things aren't parsed
               if options[:grep_hack]
                 unless options[:interesting_read_ids] or options[:interesting_node_ids]
                   raise "Programming error using bio-velvet: if :grep_hack is specified, then :interesting_read_ids or :interesting_node_ids must also be"

data/lib/bio-velvet/sequence_names.rb

@@ -0,0 +1,56 @@
+require 'tempfile'
+require 'bio-commandeer'
+require 'hopcsv'
+
+module Bio
+  module Velvet
+    # Methods for dealing with the CnyUnifiedSeq.names file output when
+    # the -create_binary flag is set in velveth.
+    class CnyUnifiedSeqNamesFile
+      # Return a hash of seqname => (Array of CnyUnifiedSeqNamesFileEntry objects)
+      # created by parsing the CnyUnifiedSeq.names file. Sometimes sequences
+      # can be found multiple times e.g. if fwd and rev of a pair is delineated
+      # after a space in the input names.
+      def self.extract_entries(path_to_cny_unified_seq_names_file, entry_names)
+        # Create results hash
+        to_return = {}
+        entry_names.each do |name|
+          to_return[name] = []
+        end
+
+        Hopcsv.foreach(path_to_cny_unified_seq_names_file,"\t") do |row|
+          name = row[0][1...row[0].length] #remove '>' at the start of the name
+          next unless to_return.key?(name) #ignore uninsteresting sequences
+
+          entry = CnyUnifiedSeqNamesFileEntry.new
+          entry.name = name
+          entry.read_id = row[1].to_i
+          entry.category = row[2].to_i
+          to_return[name].push entry
+        end
+        return to_return
+      end
+
+      # These files can be quite big, so this method
+      def self.extract_entries_using_grep_hack(path_to_cny_unified_seq_names_file, entry_names)
+        to_return = nil
+        Tempfile.open('velvet_names_grep_hack_in') do |input|
+          entry_names.each do |name|
+            input.puts ">#{name}\t"
+          end
+          input.close #flush
+
+          Tempfile.open('velvet_names_grep_hack_result') do |output|
+            Bio::Commandeer.run "grep -F -f #{input.path} #{path_to_cny_unified_seq_names_file.inspect} >#{output.path}"
+            to_return = extract_entries output.path, entry_names
+          end
+        end
+        return to_return
+      end
+    end
+
+    class CnyUnifiedSeqNamesFileEntry
+      attr_accessor :name, :read_id, :category
+    end
+  end
+end

data/lib/bio-velvet/sequences.rb

@@ -1,4 +1,4 @@
-require 'hopcsv'
+#require 'hopcsv'
 require 'bio'
 require 'tempfile'
 

data/spec/{bio-velvet_graph_spec.rb → graph_spec.rb}

@@ -254,6 +254,19 @@ describe "BioVelvet" do
     node.short_reads.collect{|r| r.read_id}.should == [47210]
   end
 
+  it 'should not parse NR when option is set' do
+    graph = Bio::Velvet::Graph.parse_from_file(
+      File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly_read_tracking','Graph2'),
+      {:dont_parse_noded_reads => true}
+      )
+    graph.should be_kind_of(Bio::Velvet::Graph)
+
+    node = graph.nodes[967]
+    node.short_reads.should == nil
+    node = graph.nodes[951]
+    node.short_reads.should == nil
+  end
+
   it 'should return sets of arcs by id' do
     graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_reads_assembly','LastGraph')
     #    ARC     2       -578    1

data/spec/sequence_names_spec.rb

@@ -0,0 +1,70 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'bio'
+
+include Bio::Velvet
+
+describe "SeqeunceNames" do
+  it 'should parse a whole file' do
+    string = <<EOF
+>read1	1	0
+>read2	2	0
+EOF
+    Tempfile.open('test') do |tempfile|
+      tempfile.print string
+      tempfile.close
+
+      names = Bio::Velvet::CnyUnifiedSeqNamesFile.extract_entries(
+        tempfile.path,
+        %w(read1 read2)
+        )
+      names.keys.should == %w(read1 read2)
+      names['read1'].kind_of?(Array).should == true
+      names['read1'].length.should == 1
+      names['read1'][0].kind_of?(Bio::Velvet::CnyUnifiedSeqNamesFileEntry).should == true
+      names['read1'].collect{|e| e.name}.should == ['read1']
+      names['read1'].collect{|e| e.read_id}.should == [1]
+      names['read1'].collect{|e| e.category}.should == [0]
+      names['read2'].collect{|e| e.name}.should == ['read2']
+      names['read2'].collect{|e| e.read_id}.should == [2]
+      names['read2'].collect{|e| e.category}.should == [0]
+    end
+  end
+
+  it 'should handle the grep hack' do
+    string = <<EOF
+>read1	1	0
+>read2	2	0
+EOF
+    Tempfile.open('test') do |tempfile|
+      tempfile.print string
+      tempfile.close
+
+      names = Bio::Velvet::CnyUnifiedSeqNamesFile.extract_entries_using_grep_hack(
+        tempfile.path,
+        %w(read1 read2)
+        )
+      names.keys.should == %w(read1 read2)
+      names['read1'].kind_of?(Array).should == true
+      names['read1'].length.should == 1
+      names['read1'][0].kind_of?(Bio::Velvet::CnyUnifiedSeqNamesFileEntry).should == true
+      names['read1'].collect{|e| e.name}.should == ['read1']
+      names['read1'].collect{|e| e.read_id}.should == [1]
+      names['read1'].collect{|e| e.category}.should == [0]
+      names['read2'].collect{|e| e.name}.should == ['read2']
+      names['read2'].collect{|e| e.read_id}.should == [2]
+      names['read2'].collect{|e| e.category}.should == [0]
+
+      names = Bio::Velvet::CnyUnifiedSeqNamesFile.extract_entries_using_grep_hack(
+        tempfile.path,
+        %w(read2)
+        )
+      names.keys.should == %w(read2)
+      names['read2'].kind_of?(Array).should == true
+      names['read2'].length.should == 1
+      names['read2'][0].kind_of?(Bio::Velvet::CnyUnifiedSeqNamesFileEntry).should == true
+      names['read2'].collect{|e| e.name}.should == ['read2']
+      names['read2'].collect{|e| e.read_id}.should == [2]
+      names['read2'].collect{|e| e.category}.should == [0]
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-01 00:00:00.000000000 Z
+date: 2014-06-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
@@ -66,6 +66,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.4'
+- !ruby/object:Gem::Dependency
+  name: bio-commandeer
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -136,6 +150,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '4.1'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
 description: Parser to work with some file formats used in the velvet DNA assembler
 email: donttrustben@gmail.com
 executables: []
@@ -155,10 +183,9 @@ files:
 - lib/bio-velvet.rb
 - lib/bio-velvet/graph.rb
 - lib/bio-velvet/runner.rb
+- lib/bio-velvet/sequence_names.rb
 - lib/bio-velvet/sequences.rb
-- spec/bio-velvet_arc_array_spec.rb
-- spec/bio-velvet_graph_spec.rb
-- spec/bio-velvet_runner_spec.rb
+- spec/arc_array_spec.rb
 - spec/data/node_sequence/LastGraph
 - spec/data/node_sequence/contigs.fa
 - spec/data/runner_input.fa
@@ -173,6 +200,9 @@ files:
 - spec/data/velvet_test_reads_assembly_read_tracking/Graph2
 - spec/data/velvet_test_reads_assembly_read_tracking/HOWTO_RECREATE
 - spec/data/velvet_test_trail_sequence_assembly/reads1.fa
+- spec/graph_spec.rb
+- spec/runner_spec.rb
+- spec/sequence_names_spec.rb
 - spec/sequences_spec.rb
 - spec/spec_helper.rb
 homepage: http://github.com/wwood/bioruby-velvet