crb-blast 0.3.1 → 0.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.gitignore +13 -0
- data/Gemfile +3 -0
- data/README.md +95 -0
- data/Rakefile +8 -0
- data/bin/crb-blast +3 -3
- data/build +1 -0
- data/crb-blast.gemspec +26 -0
- data/deps/deps.yaml +27 -0
- data/lib/crb-blast.rb +3 -447
- data/lib/crb-blast/cmd.rb +19 -0
- data/lib/crb-blast/crb-blast.rb +515 -0
- data/lib/crb-blast/hit.rb +34 -0
- data/test/helper.rb +16 -0
- data/test/query.fasta +22 -0
- data/test/query2.fasta +30 -0
- data/test/target.fasta +62 -0
- data/test/target2.fasta +76 -0
- data/test/test_bin.rb +17 -0
- data/test/test_test.rb +99 -0
- data/test/test_test2.rb +78 -0
- metadata +20 -3
- data/lib/hit.rb +0 -30
metadata
CHANGED
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@@ -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.
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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
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@@ -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-
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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
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@@ -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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203
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+
- ".gitignore"
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204
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+
- Gemfile
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205
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+
- README.md
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206
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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/
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212
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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
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data/lib/hit.rb
DELETED
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@@ -1,30 +0,0 @@
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1
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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
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