bio-nwk 0.1.0 → 0.1.1
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/lib/bio/nwk.rb +28 -0
- data/lib/bio/nwk/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
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SHA256:
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3
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-
metadata.gz:
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4
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data.tar.gz:
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3
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metadata.gz: 03f6be5c7eebbea8000cc8df4593339ecfc3ecd905b00ddb4ff17c2ccb5acc2d
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4
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data.tar.gz: eb4ed5e27f07a141d3dd9e9bac24e4f9fb979c1dd2e1070d2f43c5d10d309bef
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SHA512:
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6
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metadata.gz:
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7
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data.tar.gz:
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6
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metadata.gz: fc5f5ff47d1df75f9b0a0660345e6e8b839fd0bc5cce43201a6865681c3a0d805947a73eb6a58aab1e302194785f6514c1fac493226d580297e3ed6c2b602028
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7
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data.tar.gz: f6b20529784c8339cdb17c4ef53c69942f1b896953e8821667e4b9921a1aba520eda97a6c79f96a3111a78b74262c92fec1fe1bd6b0e82ec60023505f94d9355
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data/lib/bio/nwk.rb
CHANGED
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@@ -120,6 +120,34 @@ class Bio::Tree
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120
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end
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end
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123
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def getAlldistances()
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124
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distances = Array.new
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125
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each_edge do |node0, node1, edge|
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next if node0 == root or node1 == root
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distances << edge.distance
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128
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end
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return(distances)
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end
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132
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def normalizeBranchLength!()
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133
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min, max = getAlldistances().minmax
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134
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each_edge do |node0, node1, edge|
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135
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edge.distance = (edge.distance-min+1e-10).to_f/(max-min)
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end
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end
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def normalizeBranchLengthGainAndLoss!()
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min, max = getAlldistances().select{|i|i>=0}.minmax
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each_edge do |node0, node1, edge|
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edge.distance = (edge.distance-min+1e-10).to_f/(max-min) + 1 if edge.distance >= 0
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143
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end
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min, max = getAlldistances().select{|i|i<0}.minmax
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146
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each_edge do |node0, node1, edge|
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edge.distance = (edge.distance-min+1e-10).to_f/(max-min) if edge.distance < 0
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end
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149
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end
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150
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private
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def translate
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# TRANSLATE
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data/lib/bio/nwk/version.rb
CHANGED