iroki 0.0.5 → 0.0.6
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/README.md +4 -0
- data/exe/newick_to_phyloxml +36 -8
- data/lib/iroki/version.rb +1 -1
- 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: c3b375398b510f08d8c97c4361a2996788abd2bb
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4
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data.tar.gz: b109a3a6bacea94e8aaa32c9d316a1fafb1bb899
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e92f0e993c5ffe7a1e7c767f33ff888d15ad4ef68695c14c2848c8d18c6f18fb860f3245677be5593bf24d821a786680c9de78be90734a05823301dd8d32f5b6
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7
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data.tar.gz: e1336a5681c508bb861dee39a7d4ddebc1137d5f3ef5bc27ca703b9cc2de143ef36e6a90c84f27f35be5230afb69cdf6b0a9d25e1b48575517f485509b73cb8c
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data/README.md
CHANGED
data/exe/newick_to_phyloxml
CHANGED
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@@ -1,5 +1,10 @@
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#!/usr/bin/env ruby
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# NOTE make sure the newick has no spaces for jsPhyloXML
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# NOTE for Archaeopteryx, you need <name>#{boot}</name> to show
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# bootsraps, but for jsPhyloXML, just the confidence is needed
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require "set"
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require "bio"
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10
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@@ -24,22 +29,39 @@ $xml_end = %q{</clade>
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</phyloxml>
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}
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-
added_nodes = Set.new
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-
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def leaf? tree, node
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tree.descendents(node).count.zero?
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end
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def make_xml_string descendents
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def make_xml_string descendents, start_node
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while (node = descendents.shift)
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unless $already_added.include? node
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if leaf? $tree, node
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-
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# TODO this will raise something if no dist, rescue it
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dist = $tree.distance(start_node, node)
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$xml_start << "<clade>
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<name>#{node.name}</name>
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<branch_length>#{dist}</branch_length>
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</clade>\n"
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$already_added << node
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$prev_node = node
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else
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boot = node.bootstrap
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if boot
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boot_xml = %Q{<confidence type="bootstrap">#{boot}</confidence>}
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else
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boot_xml = ""
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end
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# TODO this will raise something if no dist, rescue it
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dist = $tree.distance(start_node, node)
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$xml_start << "<clade>
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<branch_length>#{dist}</branch_length>
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#{boot_xml}"
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STDERR.puts "LOG -- recurse"
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$
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make_xml_string $tree.descendents(node)
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make_xml_string $tree.descendents(node), node
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$xml_start << "</clade>\n"
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$already_added << node
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end
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@@ -49,9 +71,15 @@ end
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$already_added = Set.new
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-
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STDERR.puts $tree.nodes.inspect
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start_node = $tree.root
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$descendents = $tree.descendents(start_node)
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STDERR.puts $descendents.inspect
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make_xml_string $descendents
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make_xml_string $descendents, start_node
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puts $xml_start
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puts "#{$xml_end}"
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data/lib/iroki/version.rb
CHANGED