bio-polyploid-tools 0.4.1 → 0.4.2
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/VERSION +1 -1
- data/bio-polyploid-tools.gemspec +2 -2
- data/lib/bio/BIOExtensions.rb +89 -0
- metadata +1 -1
checksums.yaml
CHANGED
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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: 1cc46774ab2f15eaee35b984c144c44c122802ef
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data.tar.gz: 36ab34ac34994a67bd56eb9748a6106bffd3045f
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 9d08e9a320ce0994620c3687915f96cb7badf54a59f8ec3fda15bdc7497638d6d2dac815d8eadb2ac9d279b0fb781cc8d4e284dd6542cdc89a0b579b183f804a
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data.tar.gz: 24e83bd8221a30a89f0307bfa6079b7876ea9af135192093af89cae9fd29f643022a5b02de5152faa2f9d0846fed9077e1667460674122bb0c4b12be2cfd4c75
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data/VERSION
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@@ -1 +1 @@
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1
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0.4.
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1
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0.4.2
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data/bio-polyploid-tools.gemspec
CHANGED
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@@ -2,11 +2,11 @@
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: bio-polyploid-tools 0.4.
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# stub: bio-polyploid-tools 0.4.2 ruby lib
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Gem::Specification.new do |s|
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s.name = "bio-polyploid-tools"
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s.version = "0.4.
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s.version = "0.4.2"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.require_paths = ["lib"]
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data/lib/bio/BIOExtensions.rb
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@@ -62,3 +62,92 @@ class Hash
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end
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class Bio::NucleicAcid
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IUPAC_CODES = {
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68
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'y' => 'ct',
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'r' => 'ag',
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'w' => 'at',
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's' => 'cg',
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'k' => 'gt',
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'm' => 'ac',
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'b' => 'cgt',
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'd' => 'agt',
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'h' => 'act',
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'v' => 'acg',
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'n' => 'acgt',
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'a' => 'a',
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't' => 't',
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'g' => 'g',
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'c' => 'c',
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'u' => 'u',
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'ct' => 'y',
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'ag' => 'r',
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'at' => 'w',
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'cg' => 's',
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'gt' => 'k',
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'ac' => 'm',
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'cgt' => 'b',
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'agt' => 'd',
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'act' => 'h',
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'acg' => 'v',
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'acgt' => 'n'
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}
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def self.is_unambiguous(base)
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"acgtACGT".match(base)
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end
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def self.to_IUAPC(bases)
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base = IUPAC_CODES[bases.to_s.downcase.chars.sort.uniq.join]
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if base == nil
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p "Invalid base! #{base}"
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base = 'n' #This is a patch... as one of the scripts failed here.
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end
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base.upcase
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end
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def self.is_valid(code, base)
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IUPAC_CODES[code.downcase].chars.include? base.downcase
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end
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end
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#Monkey patching to Bio::Sequence to find snps between sequences. It assumes the
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#sequences are already aligned and doesn't check if a base on the first sequence is
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#valid on the second.
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class Bio::Sequence
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def self.snps_between(seq1, seq2)
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snps=0
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for i in (0..seq1.size-1)
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snps += 1 if seq1[i] != seq2[i]
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end
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snps
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end
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end
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class String
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#Monkey patching to count how many ambiguity codes are present in the string, for Nucleic Acids
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def count_ambiguities
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snps=0
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for i in (0..self.size-1)
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snps += 1 if !Bio::NucleicAcid.is_unambiguous(self[i])
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end
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snps
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end
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149
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#Counts how many bases are uppercase
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def upper_case_count
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match(/[^A-Z]*/).to_s.size
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end
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end
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