bio-velvet 0.3.0 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 924a25a11fbacfdcc24f2ec68bf435efbe1a2502
+  metadata.gz: b5c57762cbeea6210a80415e335e38894efc69aa
+  data.tar.gz: 9a8aba9cfb9a98b76679b025e0833ca366554e18
 SHA512:
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+  metadata.gz: 7deb192d00d7c4a8461c2e6953a1529ed9b66d2f5191840b71fcbe78d953f1f35c0f807ee62e572af0b6d196e961700d5fb45d1dfa181af054803e3d280478f8
+  data.tar.gz: 7938fc6ecdacb84be8b1720fe00cdeff46f2d8edb4a866bbe9fe0d0b449ab275275f0dc5c2453276dac1e54e30bc3eb312a3db099536c11b67e7d698cf6c1df6

data/README.md

@@ -21,6 +21,8 @@ velvet_result = Bio::Velvet::Runner.new.velvet(87, '-short /path/to/reads.fa') #
 
 contigs_file = velvet_result.contigs_path #=> path to contigs file as a String
 lastgraph_file = velvet_result.last_graph_path #=> path to last graph file as a String
+
+Bio::Velvet::Runner.new.binary_version #=> e.g. "1.2.08"
 ```
 
 By default, the ```velvet``` method passes no parameters to ```velvetg``` other than the velvet directory created by velveth. This directory is a temporary directory by default, but this can also be set. For instance, to run velvet using with a ```-cov_cutoff``` parameter in the ```velvet_dir``` directory:

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.4.0

data/lib/bio-velvet/runner.rb

@@ -24,7 +24,7 @@ module Bio
         result = Result.new
         outdir = nil
         if options[:output_assembly_path]
-          log.debug "Using pre-defined assembly directory: #{options[:output_assembly_path]}"
+          log.debug "Using pre-defined assembly directory: #{options[:output_assembly_path] }"
           outdir = options[:output_assembly_path]
         else
           outdir = Files.create.root
@@ -45,7 +45,8 @@ module Bio
       end
 
       # Run velvetg, with a Bio::Velvet::Result object
-      # generated with velveth
+      # generated with velveth, and velvetg arguments as a String (no need to specify the velvet directory, just the extra
+      # arguments).
       def velvetg(velveth_result_object, velvetg_arguments)
         cmd = "velvetg #{velveth_result_object.result_directory} #{velvetg_arguments}"
         log.info "Running velvetg: #{cmd}" if log.info?
@@ -58,6 +59,23 @@ module Bio
 
         return velveth_result_object
       end
+
+      # Detect the binary version currently in use and return
+      # as a String
+      def binary_version
+        cmd = 'velveth'
+        log.info "Running velveth: #{cmd}" if log.info?
+        status, stdout, stderr = systemu cmd
+        if status.exitstatus != 0
+          raise VelvetRunnerException, "Error running velveth: #{stderr}\n#{stdout}"
+        end
+        splits = stdout.split("\n")
+        if splits.length > 1 and matches = splits[1].match(/^Version (.+)$/)
+          return matches[1]
+        else
+          raise "Unable to parse the version number from running `#{cmd}', the output was: #{stdout}"
+        end
+      end
     end
 
     class VelvetRunnerException < Exception; end

data/spec/runner_spec.rb

@@ -18,7 +18,7 @@ describe "BioVelvet" do
       ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
       GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
       ACTATGCTGGTATTTCACTTCCAGGTACAGG'+"\n"
-    exp.gsub!(/ /,'')
+    exp.gsub!(/ / ,'')
 
     File.open(contigs_path).read.should == exp
 
@@ -51,7 +51,7 @@ describe "BioVelvet" do
       ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
       GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
       ACTATGCTGGTATTTCACTTCCAGGTACAGG'+"\n"
-    exp.gsub!(/ /,'')
+    exp.gsub!(/ / ,'')
 
     File.open(contigs_path).read.should == exp
 
@@ -64,4 +64,8 @@ describe "BioVelvet" do
     FileUtils.remove_entry_secure(result.result_directory, true)
     File.exist?(outdir).should == false
   end
+
+  it 'should detect binary_version' do
+    Bio::Velvet::Runner.new.binary_version.match(/^1\..+/).should_not be_nil #will velvet every make it out of version 1.X ? If so, this test will fail.
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.0
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-10 00:00:00.000000000 Z
+date: 2014-06-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger