tree_clusters 0.3.0 → 0.3.1
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/.gitignore +2 -1
- data/exe/snazzy_clades +58 -0
- data/lib/tree_clusters/version.rb +1 -1
- metadata +4 -2
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: aff432c29c55d5fd28f066c9ed7bf55a739c5998
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data.tar.gz: fc9599b6de682c51759b7d783ee4cc02babc50f2
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e82e143d16cac1de4446ba5422e26961f6a90b964ef12244661cdb11757dd9758019e0133f0ca56caee4a29f7ede08f0e92091a7ce4f727c22b6f446f9611408
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7
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data.tar.gz: e467648f859f638b3fd620d4a8dd843de702fc164a58359408de9c7dddf554fdbeec1ff9786e42436d5f4ae30dfe9a94320fcd7e14631f820176dd0f38cbd56b
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data/.gitignore
CHANGED
data/exe/snazzy_clades
ADDED
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@@ -0,0 +1,58 @@
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#!/usr/bin/env ruby
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Signal.trap("PIPE", "EXIT")
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require "tree_clusters"
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require "trollop"
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opts = Trollop.options do
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version TreeClusters::VERSION
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banner <<-EOS
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Lala.
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Options:
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EOS
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opt(:tree,
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"Newick tree file",
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type: :string)
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opt(:mapping,
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"Mapping file",
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type: :string)
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opt(:outdir,
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"Output directory",
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default: ".")
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opt(:base,
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"Basename for output",
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default: "snazzy_clades")
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end
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TreeClusters.extend TreeClusters
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tree = NewickTree.fromFile opts[:tree]
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metadata = TreeClusters.read_mapping_file opts[:mapping]
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snazzy_clades = TreeClusters.snazzy_clades tree, metadata
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clades_fname = File.join opts[:outdir],
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"#{opts[:base]}.snazzy_clades.txt"
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members_fname = File.join opts[:outdir],
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"#{opts[:base]}.snazzy_clades_clade_members.txt"
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File.open(clades_fname, "w") do |info_f|
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File.open(members_fname, "w") do |members_f|
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snazzy_clades.each_with_index do |(clade, info), idx|
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clade_id = "clade_#{idx+1}___#{clade.name}"
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info_f.puts [clade_id,
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info.count,
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info.map { |pair| pair.join("|")}].join "\t"
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members_f.puts [clade_id,
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clade.all_leaves.count,
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clade.all_leaves].join "\t"
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end
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end
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end
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metadata
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@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: tree_clusters
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version: !ruby/object:Gem::Version
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version: 0.3.
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version: 0.3.1
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platform: ruby
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authors:
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- Ryan Moore
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@@ -137,7 +137,8 @@ dependencies:
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description: Snazzy code for working with each cluster in a tree.
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email:
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- moorer@udel.edu
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executables:
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executables:
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- snazzy_clades
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extensions: []
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extra_rdoc_files: []
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files:
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@@ -151,6 +152,7 @@ files:
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- Rakefile
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- bin/console
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- bin/setup
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- exe/snazzy_clades
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- lib/tree_clusters.rb
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- lib/tree_clusters/version.rb
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- test_files/non_bifurcating.aln
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