tree_clusters 0.3.1 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: fc9599b6de682c51759b7d783ee4cc02babc50f2
+  metadata.gz: ea8e2199383e573da42d0a6d265b446de07bea4c
+  data.tar.gz: 775d0ace4a7398438ed4c4a34504ae9d7128d7c1
 SHA512:
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+  metadata.gz: db7302cad104d6ae05e10a4f02b1880016ba9a960cb44209d283cf9c5d730dc39ebd26a6cf64d40bd0e516d6253692112615bde41dc0e1e935ee0bc582cb36c4
+  data.tar.gz: 8dbb10b889de0f3c7db92d2138c89bdcf5357279daadaf12c97ac2e7d9b74980e3e9219308e4bb3252c93bb92b9230d77e5dc166ebd5633f36e949a54c72ca94

data/.gitignore

@@ -19,6 +19,8 @@ test_files/ignore
 
 snazzy_clades.*
 
+TEST
+
 # rspec failure tracking
 .rspec_status
 *.lock

data/.travis.yml

@@ -1,7 +1,6 @@
 sudo: false
 language: ruby
 rvm:
-  - 2.0
   - 2.1
   - 2.2
   - 2.3

data/exe/snazzy_clades_key_cols

@@ -0,0 +1,146 @@
+#!/usr/bin/env ruby
+
+Signal.trap("PIPE", "EXIT")
+
+require "tree_clusters"
+require "trollop"
+require "parse_fasta"
+require "shannon"
+require "fileutils"
+
+def get_low_ent_cols leaves, leaf2attrs, entropy_cutoff
+  low_ent_cols = []
+  alns = leaf2attrs.attrs leaves, :aln
+  aln_cols = alns.transpose
+
+  aln_cols.each_with_index do |aln_col, aln_col_idx|
+    has_gaps = aln_col.any? { |aa| aa == "-" }
+    low_entropy = Shannon::entropy(aln_col.join) <= entropy_cutoff
+
+    if !has_gaps && low_entropy
+      low_ent_cols << (aln_col_idx + 1)
+    end
+  end
+
+  Set.new low_ent_cols
+end
+
+opts = Trollop.options do
+  version TreeClusters::VERSION
+
+  banner <<-EOS
+
+  Note that if a clade's parent would be the root of the tree, no
+  columns will be subtracted when removing the parent columns as it
+  would be the entire alignment.
+
+  Options:
+  EOS
+
+  opt(:tree,
+      "Newick tree file",
+      type: :string)
+  opt(:mapping,
+      "Mapping file",
+      type: :string)
+  opt(:aln,
+      "Alignment file",
+      type: :string)
+
+  opt(:entropy_cutoff,
+      "Cutoff to consider a column low entropy",
+      default: 0.0)
+  opt(:clade_size_cutoff,
+      "Consider only clades with at least this many leaves",
+      default: 1)
+
+  opt(:outdir,
+      "Output directory",
+      default: ".")
+  opt(:base,
+      "Basename for output",
+      default: "snazzy_clades")
+end
+
+FileUtils.mkdir_p opts[:outdir]
+
+TreeClusters.extend TreeClusters
+
+tree          = NewickTree.fromFile opts[:tree]
+metadata      = TreeClusters.read_mapping_file opts[:mapping]
+snazzy_clades = TreeClusters.snazzy_clades tree, metadata
+
+aln_len = nil
+leaf2attrs = TreeClusters::Attrs.new
+ParseFasta::SeqFile.open(opts[:aln]).each_record do |rec|
+  leaf2attrs[rec.id] = { aln: rec.seq.chars }
+
+  aln_len ||= rec.seq.length
+
+  abort_unless aln_len == rec.seq.length,
+               "Aln len mismatch for #{rec.id}"
+end
+
+
+clades_fname  = File.join opts[:outdir],
+                          "#{opts[:base]}.snazzy_clades.txt"
+members_fname = File.join opts[:outdir],
+                          "#{opts[:base]}.snazzy_clades_clade_members.txt"
+all_key_cols_fname = File.join opts[:outdir],
+                               "#{opts[:base]}.snazzy_clades_key_cols.txt"
+key_cols_fname = File.join opts[:outdir],
+                               "#{opts[:base]}.snazzy_clades_key_cols.txt"
+key_cols_minus_parent_cols_fname = File.join opts[:outdir],
+                               "#{opts[:base]}.snazzy_clades_key_cols_minus_parent_cols.txt"
+key_cols_minus_sibling_cols_fname = File.join opts[:outdir],
+                               "#{opts[:base]}.snazzy_clades_key_cols_minus_sibling_cols.txt"
+
+info_f                        = File.open(clades_fname, "w")
+clade_members_f               = File.open(members_fname, "w")
+key_cols_f                    = File.open(key_cols_fname, "w")
+key_cols_minus_parent_cols_f  = File.open(key_cols_minus_parent_cols_fname, "w")
+key_cols_minus_sibling_cols_f = File.open(key_cols_minus_sibling_cols_fname, "w")
+
+begin
+  # info is { metadata_category => metadata_tag , ... }
+  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"
+
+    clade_members_f.puts [clade_id,
+                          clade.all_leaves.count,
+                          clade.all_leaves].join "\t"
+
+    key_cols_all_leaves =
+      get_low_ent_cols clade.all_leaves, leaf2attrs, opts[:entropy_cutoff]
+    key_cols_all_sibling_leaves =
+      get_low_ent_cols clade.all_sibling_leaves, leaf2attrs, opts[:entropy_cutoff]
+    key_cols_parent_leaves =
+      get_low_ent_cols clade.parent_leaves, leaf2attrs, opts[:entropy_cutoff]
+
+    key_cols_all_minus_sibling =
+      key_cols_all_leaves - key_cols_all_sibling_leaves
+    key_cols_all_minus_parent =
+      key_cols_all_leaves - key_cols_parent_leaves
+
+    key_cols_f.puts [clade_id,
+                     key_cols_all_leaves.count,
+                     key_cols_all_leaves.to_a].join "\t"
+    key_cols_minus_parent_cols_f.puts [clade_id,
+                                       key_cols_all_minus_parent.count,
+                                       key_cols_all_minus_parent.to_a].join "\t"
+    key_cols_minus_sibling_cols_f.puts [clade_id,
+                                        key_cols_all_minus_sibling.count,
+                                        key_cols_all_minus_sibling.to_a].join "\t"
+
+  end
+ensure
+  info_f.close
+  clade_members_f.close
+  key_cols_f.close
+  key_cols_minus_parent_cols_f.close
+  key_cols_minus_sibling_cols_f.close
+end

data/lib/tree_clusters/version.rb

@@ -1,3 +1,3 @@
 module TreeClusters
-  VERSION = "0.3.1"
+  VERSION = "0.4.0"
 end

data/test_files/small.aln

@@ -0,0 +1,14 @@
+>a-1
+AAAA
+>a-2
+AAAT
+>b-1
+CCCC
+>b-2
+CCCT
+>bb-1
+CCTG
+>bbb-1
+CCGG
+>bbb-2
+CGGG

data/tree_clusters.gemspec

@@ -30,5 +30,7 @@ Gem::Specification.new do |spec|
 
   spec.add_runtime_dependency "abort_if", "~> 0.2.0"
   spec.add_runtime_dependency "newick-ruby", "~> 1.0", ">= 1.0.4"
+  spec.add_runtime_dependency "parse_fasta", "~> 2.3"
+  spec.add_runtime_dependency "shannon", "~> 0.1", ">= 0.1.1"
   spec.add_runtime_dependency "trollop", "~> 2.1", ">= 2.1.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: tree_clusters
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.4.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-11-01 00:00:00.000000000 Z
+date: 2017-11-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -114,6 +114,40 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.4
+- !ruby/object:Gem::Dependency
+  name: parse_fasta
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.3'
+- !ruby/object:Gem::Dependency
+  name: shannon
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.1
 - !ruby/object:Gem::Dependency
   name: trollop
   requirement: !ruby/object:Gem::Requirement
@@ -139,6 +173,7 @@ email:
 - moorer@udel.edu
 executables:
 - snazzy_clades
+- snazzy_clades_key_cols
 extensions: []
 extra_rdoc_files: []
 files:
@@ -153,10 +188,12 @@ files:
 - bin/console
 - bin/setup
 - exe/snazzy_clades
+- exe/snazzy_clades_key_cols
 - lib/tree_clusters.rb
 - lib/tree_clusters/version.rb
 - test_files/non_bifurcating.aln
 - test_files/non_bifurcating.tre
+- test_files/small.aln
 - test_files/small.mapping
 - test_files/small.tre
 - test_files/test.tre