aai 0.2.1 → 0.2.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 74c4793c46883e92fab311837cf8b9ffd74b116d
+  metadata.gz: 9bac62037fd410a0529a22d1c010d10ce7839633
+  data.tar.gz: 2ea10d1fb86cab89108ffdda9b09971cff7950bd
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+  metadata.gz: cc31bb1eb4cec4a1071ec9d17e9f993fa833dd9fae6bc676bbeec4dedcd711b8e4d494ca5370597029fd1f29e16af61726e556661ba13c73251834789dc0147d
+  data.tar.gz: 93305b9087bbba596f0a37edc6df2086d4d96af0a5161ca520614c2dff8ad21eae79da0e60b533859309b3e60b050d6295f0ef38555f2d472f290b6f8d984478

data/.gitignore

@@ -10,3 +10,5 @@
 
 # rspec failure tracking
 .rspec_status
+.ruby-version
+.ruby-gemset

data/.travis.yml

@@ -10,7 +10,6 @@ rvm:
 addons:
   apt:
     packages:
-    - parallel
     - ncbi-blast+
 
 before_install:

data/aai.gemspec

@@ -28,6 +28,7 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "yard", "~> 0.9.9"
 
   spec.add_runtime_dependency "abort_if", "~> 0.2.0"
+  spec.add_runtime_dependency "parallel", "~> 1.6", ">= 1.6.1"
   spec.add_runtime_dependency "parse_fasta", "~> 2.2"
   spec.add_runtime_dependency "systemu", "~> 2.6", ">= 2.6.5"
   spec.add_runtime_dependency "trollop", "~> 2.1", ">= 2.1.2"

data/exe/aai

@@ -13,7 +13,11 @@ include AbortIf::Assert
 Aai.extend Aai
 Aai.extend Aai::Utils
 
-version_banner =
+def move_files fnames, dest
+  fnames.each do |fname|
+    FileUtils.mv fname, dest
+  end
+end
 
 opts = Trollop.options do
   version Aai::VERSION_BANNER
@@ -60,9 +64,24 @@ two_way = Aai.two_way_aai best_hits
 
 aai_strings = Aai.aai_strings one_way, two_way
 
-outf = File.join opts[:outdir], "#{opts[:basename]}.aai.txt"
+score_dir = File.join opts[:outdir], "aai_scores"
+FileUtils.mkdir_p score_dir
+outf = File.join score_dir, "#{opts[:basename]}.aai.txt"
 File.open(outf, "w") do |f|
   Aai.aai_strings(one_way, two_way).each do |str|
     f.puts str
   end
 end
+
+blast_db_dir = File.join opts[:outdir], "blastdbs"
+btab_dir = File.join opts[:outdir], "btabs"
+clean_fasta_dir = File.join opts[:outdir], "clean_fastas"
+
+FileUtils.mkdir_p [blast_db_dir, btab_dir, clean_fasta_dir]
+
+move_files clean_fnames, clean_fasta_dir
+move_files btabs, btab_dir
+
+blast_db_basenames.each do |basename|
+  move_files Dir.glob("#{basename}*"), blast_db_dir
+end

data/lib/aai.rb

@@ -1,5 +1,6 @@
 require "abort_if"
 require "systemu"
+require "parallel"
 require "parse_fasta"
 
 require "aai/core_extensions"
@@ -8,6 +9,7 @@ require "aai/version"
 
 AbortIf.extend AbortIf
 Process.extend Aai::CoreExtensions::Process
+Time.extend Aai::CoreExtensions::Time
 
 module Aai
   include Utils
@@ -47,10 +49,20 @@ module Aai
       "#{f1}____#{f2}.aai_blastp"
     end
 
-    title = "Running blast jobs"
-    cmd = %Q{parallel --xapply "blastp -outfmt 6 -query {1} -db {2} -out {3} -evalue 1e-3" ::: #{first_files.join " "} ::: #{second_files.join " "} ::: #{outf_names.join " "}}
+    parallel_args = first_files.length.times.map do |idx|
+      [first_files[idx], second_files[idx], outf_names[idx]]
+    end
+
+    Time.time_it "Running blast jobs" do
+      Parallel.each(parallel_args) do |infiles|
+        query = infiles[0]
+        db    = infiles[1]
+        out   = infiles[2]
 
-    Process.run_and_time_it! title, cmd
+        cmd = "blastp -outfmt 6 -query #{query} -db #{db} -out #{out} -evalue #{EVALUE_CUTOFF}"
+        Process.run_it! cmd
+      end
+    end
 
     outf_names
   end
@@ -64,10 +76,13 @@ module Aai
     suffix = BLAST_DB_SUFFIX
     outfiles = fnames.map { |fname| fname + suffix }
 
-    title = "Making blast databases"
-    cmd = %Q{parallel "makeblastdb -in {} -out {}#{BLAST_DB_SUFFIX} -dbtype prot" ::: #{fnames.join " "}}
+    Time.time_it "Making blast databases" do
+      Parallel.each(fnames) do |fname|
+        cmd = "makeblastdb -in #{fname} -out #{fname}#{BLAST_DB_SUFFIX} -dbtype prot"
 
-    Process.run_and_time_it! title, cmd
+        Process.run_it! cmd
+      end
+    end
 
     outfiles
   end

data/lib/aai/version.rb

@@ -1,5 +1,5 @@
 module Aai
-  VERSION = "0.2.1"
+  VERSION = "0.2.2"
   COPYRIGHT = "2017 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/aai"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: aai
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-06-22 00:00:00.000000000 Z
+date: 2017-06-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -94,6 +94,26 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: parallel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.6.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.6.1
 - !ruby/object:Gem::Dependency
   name: parse_fasta
   requirement: !ruby/object:Gem::Requirement