tree_clusters 0.3.0 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 884a3b714acdf6b5b933c89ce0d6a82aaf9bcbca
-  data.tar.gz: 1e3573ead3b5ad82149cec6ccbdf8a8b94eb9939
+  metadata.gz: aff432c29c55d5fd28f066c9ed7bf55a739c5998
+  data.tar.gz: fc9599b6de682c51759b7d783ee4cc02babc50f2
 SHA512:
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-  data.tar.gz: aea3b7dab128fbf1d08e6cd0ac813cc415652d2586f8be80c696f8946ac447b0251b1bbbc61acbd2f85760ab7452ae65db781f98d1d30d1feb2e02c93727d1fe
+  metadata.gz: e82e143d16cac1de4446ba5422e26961f6a90b964ef12244661cdb11757dd9758019e0133f0ca56caee4a29f7ede08f0e92091a7ce4f727c22b6f446f9611408
+  data.tar.gz: e467648f859f638b3fd620d4a8dd843de702fc164a58359408de9c7dddf554fdbeec1ff9786e42436d5f4ae30dfe9a94320fcd7e14631f820176dd0f38cbd56b

data/.gitignore

@@ -17,7 +17,8 @@ test_files/ignore
 
 .ruby-*
 
-snazzy_clades*
+snazzy_clades.*
 
 # rspec failure tracking
 .rspec_status
+*.lock

data/exe/snazzy_clades

@@ -0,0 +1,58 @@
+#!/usr/bin/env ruby
+
+Signal.trap("PIPE", "EXIT")
+
+require "tree_clusters"
+require "trollop"
+
+opts = Trollop.options do
+  version TreeClusters::VERSION
+
+  banner <<-EOS
+
+  Lala.
+
+  Options:
+  EOS
+
+  opt(:tree,
+      "Newick tree file",
+      type: :string)
+  opt(:mapping,
+      "Mapping file",
+      type: :string)
+
+  opt(:outdir,
+      "Output directory",
+      default: ".")
+  opt(:base,
+      "Basename for output",
+      default: "snazzy_clades")
+end
+
+TreeClusters.extend TreeClusters
+
+tree          = NewickTree.fromFile opts[:tree]
+metadata      = TreeClusters.read_mapping_file opts[:mapping]
+snazzy_clades = TreeClusters.snazzy_clades tree, metadata
+
+clades_fname  = File.join opts[:outdir],
+                          "#{opts[:base]}.snazzy_clades.txt"
+members_fname = File.join opts[:outdir],
+                          "#{opts[:base]}.snazzy_clades_clade_members.txt"
+
+File.open(clades_fname, "w") do |info_f|
+  File.open(members_fname, "w") do |members_f|
+    snazzy_clades.each_with_index do |(clade, info), idx|
+      clade_id = "clade_#{idx+1}___#{clade.name}"
+
+      info_f.puts [clade_id,
+                   info.count,
+                   info.map { |pair| pair.join("|")}].join "\t"
+
+      members_f.puts [clade_id,
+                      clade.all_leaves.count,
+                      clade.all_leaves].join "\t"
+    end
+  end
+end

data/lib/tree_clusters/version.rb

@@ -1,3 +1,3 @@
 module TreeClusters
-  VERSION = "0.3.0"
+  VERSION = "0.3.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: tree_clusters
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
 platform: ruby
 authors:
 - Ryan Moore
@@ -137,7 +137,8 @@ dependencies:
 description: Snazzy code for working with each cluster in a tree.
 email:
 - moorer@udel.edu
-executables: []
+executables:
+- snazzy_clades
 extensions: []
 extra_rdoc_files: []
 files:
@@ -151,6 +152,7 @@ files:
 - Rakefile
 - bin/console
 - bin/setup
+- exe/snazzy_clades
 - lib/tree_clusters.rb
 - lib/tree_clusters/version.rb
 - test_files/non_bifurcating.aln