iroki 0.0.4 → 0.0.5
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/.gitignore +1 -0
- data/README.md +20 -0
- data/exe/newick_to_phyloxml +57 -0
- data/lib/iroki/version.rb +1 -1
- metadata +4 -2
checksums.yaml
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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: 9b9b21077f245bb5dd166b189504376da92112db
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data.tar.gz: 8ccd71597ff5d2f231a7b3d689df1f37b82a5902
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SHA512:
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metadata.gz:
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metadata.gz: ffb3938259ced78bc637f5ddd95378b61a79c24d3c0b97997e616ab906b2dd281720f5273cf1291b7ccf8b2f4ceb7b6686b5a62bb75a55ec8aa6044e1d6f91c1
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data.tar.gz: 7b896d9575a1ff07b97cc565e0996f7da3293df9957b0cfc566dcc2eaa7786ed172da48eccfe3cc2e3418858274b9632cca592e53aaa2f9742f6685355cf4d83
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data/.gitignore
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data/README.md
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@@ -39,6 +39,18 @@ Or install it yourself as:
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$ gem install iroki
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## Other programs ##
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### Newick format to PhyloXML ###
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- `exe/newick_to_phyloxml`
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This will be installed when you run `gem install iroki`.
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*Usage*: `newick_to_phyloxml tree.newick > tree.phyloxml`
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*Note*: No specs for this as of yet.
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## Development ##
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After checking out the repo, run `bin/setup` to install
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@@ -76,3 +88,11 @@ executable, and use RubyGems for installation.
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### 0.0.3 ###
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Add a [Dockerfile](https://github.com/mooreryan/iroki/blob/master/Dockerfile) and a [wrapper script](https://github.com/mooreryan/iroki/blob/master/exe/iroki_docker) for running Iroki with Docker.
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### 0.0.4 ###
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Fix the `iroki_docker` install bug.
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### 0.0.5 ###
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Add `newick_to_phyloxml` script.
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@@ -0,0 +1,57 @@
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#!/usr/bin/env ruby
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require "set"
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require "bio"
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def leaf? tree, node
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tree.children(node).empty?
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end
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newick = ARGV.first
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treeio = Bio::FlatFile.open(Bio::Newick, newick)
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newick = treeio.next_entry
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$tree = newick.tree
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$xml_start = %q{<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
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<phylogeny rooted="false">
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<clade>
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}
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$xml_end = %q{</clade>
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</phylogeny>
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</phyloxml>
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}
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added_nodes = Set.new
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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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while (node = descendents.shift)
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unless $already_added.include? node
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if leaf? $tree, node
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$xml_start << "<clade>\n<name>#{node.name}</name>\n</clade>\n"
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$already_added << node
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else
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STDERR.puts "LOG -- recurse"
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$xml_start << "<clade>\n"
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make_xml_string $tree.descendents(node)
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$xml_start << "</clade>\n"
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$already_added << node
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end
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end
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end
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end
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$already_added = Set.new
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$descendents = $tree.descendents($tree.root)
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make_xml_string $descendents
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puts $xml_start
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puts "#{$xml_end}"
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data/lib/iroki/version.rb
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metadata
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: iroki
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version: !ruby/object:Gem::Version
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version: 0.0.
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version: 0.0.5
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platform: ruby
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authors:
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- Ryan Moore
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autorequire:
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bindir: exe
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cert_chain: []
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date: 2016-05-
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date: 2016-05-22 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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@@ -154,6 +154,7 @@ email:
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- moorer@udel.edu
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executables:
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- iroki
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- newick_to_phyloxml
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extensions: []
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extra_rdoc_files: []
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files:
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- bin/iroki_docker
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- bin/setup
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- exe/iroki
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- exe/newick_to_phyloxml
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- iroki.gemspec
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- lib/iroki.rb
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- lib/iroki/color/color.rb
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