tree_clusters 0.3.1 → 0.4.0
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 -0
- data/.travis.yml +0 -1
- data/exe/snazzy_clades_key_cols +146 -0
- data/lib/tree_clusters/version.rb +1 -1
- data/test_files/small.aln +14 -0
- data/tree_clusters.gemspec +2 -0
- metadata +39 -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: ea8e2199383e573da42d0a6d265b446de07bea4c
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data.tar.gz: 775d0ace4a7398438ed4c4a34504ae9d7128d7c1
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: db7302cad104d6ae05e10a4f02b1880016ba9a960cb44209d283cf9c5d730dc39ebd26a6cf64d40bd0e516d6253692112615bde41dc0e1e935ee0bc582cb36c4
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data.tar.gz: 8dbb10b889de0f3c7db92d2138c89bdcf5357279daadaf12c97ac2e7d9b74980e3e9219308e4bb3252c93bb92b9230d77e5dc166ebd5633f36e949a54c72ca94
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data/.gitignore
CHANGED
data/.travis.yml
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@@ -0,0 +1,146 @@
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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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require "parse_fasta"
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require "shannon"
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require "fileutils"
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def get_low_ent_cols leaves, leaf2attrs, entropy_cutoff
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low_ent_cols = []
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alns = leaf2attrs.attrs leaves, :aln
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aln_cols = alns.transpose
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aln_cols.each_with_index do |aln_col, aln_col_idx|
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has_gaps = aln_col.any? { |aa| aa == "-" }
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low_entropy = Shannon::entropy(aln_col.join) <= entropy_cutoff
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if !has_gaps && low_entropy
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low_ent_cols << (aln_col_idx + 1)
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end
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end
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Set.new low_ent_cols
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end
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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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Note that if a clade's parent would be the root of the tree, no
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columns will be subtracted when removing the parent columns as it
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would be the entire alignment.
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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(:aln,
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"Alignment file",
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type: :string)
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opt(:entropy_cutoff,
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"Cutoff to consider a column low entropy",
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default: 0.0)
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opt(:clade_size_cutoff,
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"Consider only clades with at least this many leaves",
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default: 1)
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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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FileUtils.mkdir_p opts[:outdir]
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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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aln_len = nil
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leaf2attrs = TreeClusters::Attrs.new
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ParseFasta::SeqFile.open(opts[:aln]).each_record do |rec|
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leaf2attrs[rec.id] = { aln: rec.seq.chars }
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aln_len ||= rec.seq.length
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abort_unless aln_len == rec.seq.length,
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"Aln len mismatch for #{rec.id}"
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end
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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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all_key_cols_fname = File.join opts[:outdir],
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"#{opts[:base]}.snazzy_clades_key_cols.txt"
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key_cols_fname = File.join opts[:outdir],
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"#{opts[:base]}.snazzy_clades_key_cols.txt"
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key_cols_minus_parent_cols_fname = File.join opts[:outdir],
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"#{opts[:base]}.snazzy_clades_key_cols_minus_parent_cols.txt"
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key_cols_minus_sibling_cols_fname = File.join opts[:outdir],
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"#{opts[:base]}.snazzy_clades_key_cols_minus_sibling_cols.txt"
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info_f = File.open(clades_fname, "w")
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clade_members_f = File.open(members_fname, "w")
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key_cols_f = File.open(key_cols_fname, "w")
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key_cols_minus_parent_cols_f = File.open(key_cols_minus_parent_cols_fname, "w")
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key_cols_minus_sibling_cols_f = File.open(key_cols_minus_sibling_cols_fname, "w")
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begin
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# info is { metadata_category => metadata_tag , ... }
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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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clade_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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key_cols_all_leaves =
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get_low_ent_cols clade.all_leaves, leaf2attrs, opts[:entropy_cutoff]
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key_cols_all_sibling_leaves =
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get_low_ent_cols clade.all_sibling_leaves, leaf2attrs, opts[:entropy_cutoff]
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key_cols_parent_leaves =
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get_low_ent_cols clade.parent_leaves, leaf2attrs, opts[:entropy_cutoff]
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key_cols_all_minus_sibling =
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key_cols_all_leaves - key_cols_all_sibling_leaves
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key_cols_all_minus_parent =
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key_cols_all_leaves - key_cols_parent_leaves
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key_cols_f.puts [clade_id,
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key_cols_all_leaves.count,
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key_cols_all_leaves.to_a].join "\t"
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key_cols_minus_parent_cols_f.puts [clade_id,
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key_cols_all_minus_parent.count,
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key_cols_all_minus_parent.to_a].join "\t"
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key_cols_minus_sibling_cols_f.puts [clade_id,
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key_cols_all_minus_sibling.count,
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key_cols_all_minus_sibling.to_a].join "\t"
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end
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ensure
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info_f.close
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clade_members_f.close
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key_cols_f.close
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key_cols_minus_parent_cols_f.close
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key_cols_minus_sibling_cols_f.close
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end
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data/tree_clusters.gemspec
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spec.add_runtime_dependency "abort_if", "~> 0.2.0"
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spec.add_runtime_dependency "newick-ruby", "~> 1.0", ">= 1.0.4"
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spec.add_runtime_dependency "parse_fasta", "~> 2.3"
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spec.add_runtime_dependency "shannon", "~> 0.1", ">= 0.1.1"
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spec.add_runtime_dependency "trollop", "~> 2.1", ">= 2.1.2"
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end
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metadata
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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.
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version: 0.4.0
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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: 2017-11-
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date: 2017-11-02 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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- - ">="
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- !ruby/object:Gem::Version
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version: 1.0.4
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- !ruby/object:Gem::Dependency
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name: parse_fasta
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.3'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.3'
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- !ruby/object:Gem::Dependency
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name: shannon
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.1'
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.1.1
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.1'
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.1.1
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- !ruby/object:Gem::Dependency
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name: trollop
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requirement: !ruby/object:Gem::Requirement
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@@ -139,6 +173,7 @@ email:
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- moorer@udel.edu
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executables:
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- snazzy_clades
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- snazzy_clades_key_cols
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extensions: []
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extra_rdoc_files: []
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files:
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- bin/console
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- bin/setup
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- exe/snazzy_clades
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- exe/snazzy_clades_key_cols
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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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- test_files/non_bifurcating.tre
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- test_files/small.aln
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- test_files/small.mapping
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- test_files/small.tre
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- test_files/test.tre
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