crb-blast 0.3.1 → 0.4.0

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metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: crb-blast
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  version: !ruby/object:Gem::Version
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- version: 0.3.1
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+ version: 0.4.0
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  platform: ruby
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  authors:
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  - Chris Boursnell
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-07-18 00:00:00.000000000 Z
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+ date: 2014-07-23 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: trollop
@@ -200,9 +200,26 @@ executables:
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  extensions: []
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  extra_rdoc_files: []
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  files:
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+ - ".gitignore"
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+ - Gemfile
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+ - README.md
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+ - Rakefile
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  - bin/crb-blast
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+ - build
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+ - crb-blast.gemspec
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+ - deps/deps.yaml
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  - lib/crb-blast.rb
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- - lib/hit.rb
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+ - lib/crb-blast/cmd.rb
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+ - lib/crb-blast/crb-blast.rb
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+ - lib/crb-blast/hit.rb
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+ - test/helper.rb
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+ - test/query.fasta
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+ - test/query2.fasta
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+ - test/target.fasta
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+ - test/target2.fasta
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+ - test/test_bin.rb
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+ - test/test_test.rb
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+ - test/test_test2.rb
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  homepage: http://rubygems.org/gems/crb-blast
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  licenses:
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  - MIT
data/lib/hit.rb DELETED
@@ -1,30 +0,0 @@
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- class Hit
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- # Fields: query id, subject id, % identity, alignment length, mismatches,
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- # gap opens, q. start, q. end, s. start, s. end, evalue, bit score
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- attr_accessor :query, :target, :id, :alnlen, :mismatches, :gaps, :qstart,
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- :qend, :tstart, :tend, :evalue, :bitscore, :qlen, :tlen
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-
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- def initialize(list)
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- raise(RuntimeError, "unexpected number of columns") unless list.length==14
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- @query = list[0].split(/[\|\ ]/).first
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- @target = list[1].split(/[\|\ ]/).first
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- @id = list[2]
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- @alnlen = list[3].to_i
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- @mismatches = list[4].to_i
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- @gaps = list[5].to_i
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- @qstart = list[6].to_i
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- @qend = list[7].to_i
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- @tstart = list[8].to_i
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- @tend = list[9].to_i
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- @evalue = list[10].to_f
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- @bitscore = list[11].to_f
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- @qlen = list[12].to_f
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- @tlen = list[13].to_f
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- end
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-
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- def to_s
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- s = "#{@query}\t#{@target}\t#{@id}\t#{@alnlen}\t#{@evalue}\t#{@bitscore}\t"
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- s << "#{@qstart}..#{@qend}\t#{@tstart}..#{@tend}"
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- return s
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- end
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- end