vienna_rna 0.4.3 → 0.4.4
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- checksums.yaml +4 -4
- data/README.md +1 -1
- data/lib/vienna_rna/modules/fold.rb +1 -1
- data/lib/vienna_rna/modules/rna.rb +4 -4
- data/lib/vienna_rna/modules/subopt.rb +1 -1
- data/lib/vienna_rna/modules/xbor.rb +1 -1
- metadata +1 -1
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 7d9804f2f40ec0ae56690e373c7f9a3e6e37e2c9
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data.tar.gz: 8e0513d28b214658a90f1c0000aa09457c0dc568
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 2ca3480228c5c2356ef78c730479cc9c9b9e76761ffcb58e32f294b4910e0f8afc4c66b0493cdc4c8de521470ed09495ff6b29abd4af74a8d987e27ffcf3423c
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data.tar.gz: 6c64233272aa7cf6188a467f65e965bd589f4a15a122d8730ad3ee430ee851bb75c3152fa3584c19a03e300900cec8bf6f00050d4bbf3eaca195e9254d71dcc1
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data/README.md
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@@ -16,4 +16,4 @@ Simple use case:
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> mfe_rna = RNA("CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG").run(:fold).mfe_rna
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#=> echo CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG | rnafold --noPS
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#=> Total runtime: 0.013 sec.
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#=> #<ViennaRna::
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#=> #<ViennaRna::Rna CCUCGAGGGGAACCCGAAAG... ((((..(((...(((....) [truncated]>
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@@ -12,7 +12,7 @@ module ViennaRna
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unless data.seq.length == structure.length
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raise "Sequence: '#{data.seq}'\nStructure: '#{structure}'"
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else
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@mfe_rna, @structure, @mfe =
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@mfe_rna, @structure, @mfe = Rna.init_from_string(data.seq, structure), structure, Parser.rnafold_mfe(@response)
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end
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end
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@@ -32,7 +32,7 @@ module ViennaRna
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@structure = case structure
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when :empty then empty_structure
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when :mfe then ViennaRna::Fold.run(
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when :mfe then ViennaRna::Fold.run(Rna.init_from_string(seq)).structure
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when String then structure
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end
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end
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@@ -44,11 +44,11 @@ module ViennaRna
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def inspect
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case [sequence.present?, structure.present?]
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when [true, true] then
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"
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"#<#{self.class.name} #{seq[0, 20] + (seq.length > 20 ? '...' : '')} #{str[0, 20] + (str.length > 20 ? ' [truncated]' : '')}>"
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when [true, false] then
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"
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"#<#{self.class.name} #{seq[0, 20] + (seq.length > 20 ? '...' : '')}>"
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when [false, false] then
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"
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"#<#{self.class.name}>"
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end
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end
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@@ -3,7 +3,7 @@ module ViennaRna
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attr_reader :structures
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def post_process
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@structures = @response.split(/\n/)[1..-1].map { |output|
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@structures = @response.split(/\n/)[1..-1].map { |output| Rna.init_from_string(data.seq, output.split(/\s+/).first) }
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end
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def bin(count = 1)
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@@ -29,7 +29,7 @@ module ViennaRna
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sequence = log.split(/\n/).first.split(/\s+/)[1]
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structure = log.split(/\n/).first.split(/\s+/)[2]
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klass.bootstrap(
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klass.bootstrap(Rna.init_from_string(sequence, structure), log)
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end
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def self.parse(response)
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