iroki 0.0.5 → 0.0.6
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- 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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1
1
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---
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2
2
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SHA1:
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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: c3b375398b510f08d8c97c4361a2996788abd2bb
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4
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+
data.tar.gz: b109a3a6bacea94e8aaa32c9d316a1fafb1bb899
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5
5
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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: 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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1
1
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#!/usr/bin/env ruby
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2
2
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3
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+
# NOTE make sure the newick has no spaces for jsPhyloXML
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4
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+
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5
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+
# NOTE for Archaeopteryx, you need <name>#{boot}</name> to show
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6
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+
# bootsraps, but for jsPhyloXML, just the confidence is needed
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7
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+
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3
8
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require "set"
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4
9
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require "bio"
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5
10
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@@ -24,22 +29,39 @@ $xml_end = %q{</clade>
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24
29
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</phyloxml>
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25
30
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}
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26
31
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27
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-
added_nodes = Set.new
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28
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-
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29
32
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def leaf? tree, node
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30
33
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tree.descendents(node).count.zero?
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31
34
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end
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32
35
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33
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-
def make_xml_string descendents
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36
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+
def make_xml_string descendents, start_node
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34
37
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while (node = descendents.shift)
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35
38
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unless $already_added.include? node
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36
39
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if leaf? $tree, node
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37
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-
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40
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+
# TODO this will raise something if no dist, rescue it
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41
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+
dist = $tree.distance(start_node, node)
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|
42
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+
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43
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+
$xml_start << "<clade>
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44
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+
<name>#{node.name}</name>
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45
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+
<branch_length>#{dist}</branch_length>
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46
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+
</clade>\n"
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38
47
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$already_added << node
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48
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+
$prev_node = node
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39
49
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else
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50
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+
boot = node.bootstrap
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51
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+
if boot
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52
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+
boot_xml = %Q{<confidence type="bootstrap">#{boot}</confidence>}
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53
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+
else
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54
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+
boot_xml = ""
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55
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+
end
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56
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+
|
|
57
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+
# TODO this will raise something if no dist, rescue it
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|
58
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+
dist = $tree.distance(start_node, node)
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|
59
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+
$xml_start << "<clade>
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60
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+
<branch_length>#{dist}</branch_length>
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61
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+
#{boot_xml}"
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62
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+
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|
40
63
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STDERR.puts "LOG -- recurse"
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|
41
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-
$
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42
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-
make_xml_string $tree.descendents(node)
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64
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+
make_xml_string $tree.descendents(node), node
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43
65
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$xml_start << "</clade>\n"
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44
66
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$already_added << node
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45
67
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end
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@@ -49,9 +71,15 @@ end
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49
71
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50
72
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$already_added = Set.new
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51
73
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52
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-
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74
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+
STDERR.puts $tree.nodes.inspect
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75
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+
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76
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+
start_node = $tree.root
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77
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+
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78
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+
$descendents = $tree.descendents(start_node)
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79
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+
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80
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+
STDERR.puts $descendents.inspect
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53
81
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54
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-
make_xml_string $descendents
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82
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+
make_xml_string $descendents, start_node
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55
83
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56
84
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puts $xml_start
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57
85
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puts "#{$xml_end}"
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data/lib/iroki/version.rb
CHANGED