crb-blast 0.3.1 → 0.4.0

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: crb-blast
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.4.0
 platform: ruby
 authors:
 - Chris Boursnell
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-18 00:00:00.000000000 Z
+date: 2014-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -200,9 +200,26 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- ".gitignore"
+- Gemfile
+- README.md
+- Rakefile
 - bin/crb-blast
+- build
+- crb-blast.gemspec
+- deps/deps.yaml
 - lib/crb-blast.rb
-- lib/hit.rb
+- lib/crb-blast/cmd.rb
+- lib/crb-blast/crb-blast.rb
+- lib/crb-blast/hit.rb
+- test/helper.rb
+- test/query.fasta
+- test/query2.fasta
+- test/target.fasta
+- test/target2.fasta
+- test/test_bin.rb
+- test/test_test.rb
+- test/test_test2.rb
 homepage: http://rubygems.org/gems/crb-blast
 licenses:
 - MIT

data/lib/hit.rb

@@ -1,30 +0,0 @@
-class Hit
-  # Fields: query id, subject id, % identity, alignment length, mismatches,
-  # gap opens, q. start, q. end, s. start, s. end, evalue, bit score
-  attr_accessor :query, :target, :id, :alnlen, :mismatches, :gaps, :qstart, 
-  :qend, :tstart, :tend, :evalue, :bitscore, :qlen, :tlen
-  
-  def initialize(list)
-    raise(RuntimeError, "unexpected number of columns") unless list.length==14
-    @query      = list[0].split(/[\|\ ]/).first
-    @target     = list[1].split(/[\|\ ]/).first
-    @id         = list[2]
-    @alnlen     = list[3].to_i
-    @mismatches = list[4].to_i
-    @gaps       = list[5].to_i
-    @qstart     = list[6].to_i
-    @qend       = list[7].to_i
-    @tstart     = list[8].to_i
-    @tend       = list[9].to_i
-    @evalue     = list[10].to_f
-    @bitscore   = list[11].to_f
-    @qlen       = list[12].to_f
-    @tlen       = list[13].to_f
-  end
-
-  def to_s
-    s = "#{@query}\t#{@target}\t#{@id}\t#{@alnlen}\t#{@evalue}\t#{@bitscore}\t"
-    s << "#{@qstart}..#{@qend}\t#{@tstart}..#{@tend}"
-    return s
-  end
-end