crb-blast 0.2 → 0.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 4271f12aa93ccaa344fe8dbc1bcdecd1281ef7a1
-  data.tar.gz: 7222b48806f393e89c096ad50aaa92997dccbe9d
+  metadata.gz: fb3b123812929285b57903de865b981104ffdfe9
+  data.tar.gz: d66187a8a9b08b4bb282d03ed75898f1f5789af8
 SHA512:
-  metadata.gz: f41b2d87c4113fbb3022bfd80329c7a1224ed166c0bd3402dd15d244e1b7f69cbd6f386c6839f294a0f76e0d2adc4d7630ea59bf2dc860c06f07fedf8d4e6544
-  data.tar.gz: 2907e7327968d1edab89a3b6849e811d40e29bc8011671894708ebd656ebce1acb05e970aad0f9bfcfaddbbd2834deee9b1bb589a5e0028435c6023d1b89703d
+  metadata.gz: 260463b1df616c63dbd262fb5d0e205610d221c4d81fdf0216e28fdcf8fde7d7f821c2e10d80edec969d5d9b64288823e169d06f7235abbca7553f1a633e9fd2
+  data.tar.gz: cde2ffeb8b7efe84d6ca09f99358dc5dd7cf77f193dfc91669af7a9ba54e66712f085c9dbe26d45f7abe2e01a96f453568198b1516fedcecf2ee0f3cefcf6c70

data/bin/crb-blast

@@ -6,11 +6,12 @@
 
 require 'trollop'
 require 'crb-blast'
+require 'bindeps'
 
 opts = Trollop::options do
   banner <<-EOS
 
-CRB-Blast v0.1 by Chris Boursnell <cmb211@cam.ac.uk>
+CRB-Blast v0.3 by Chris Boursnell <cmb211@cam.ac.uk>
 
 Conditional Reciprocal Best BLAST
 
@@ -44,14 +45,22 @@ EOS
       "output file as tsv",
       :required => true,
       :type => String
+
+  opt :split,
+      "split the fasta files into chunks and run multiple blast jobs and then"+
+      "combine them."
 end
 
 Trollop::die :query, "must exist" if !File.exist?(opts[:query])
 Trollop::die :target, "must exist" if !File.exist?(opts[:target])
 
+gem_dir = Gem.loaded_specs['crb-blast'].full_gem_path
+gem_deps = File.join(gem_dir, 'deps', 'deps.yaml')
+Bindeps.require gem_deps
+
 blaster = CRB_Blast.new(opts.query, opts.target)
 dbs = blaster.makedb
-run = blaster.run_blast(opts.evalue, opts.threads)
+run = blaster.run_blast(opts.evalue, opts.threads, opts.split)
 load = blaster.load_outputs
 recips = blaster.find_reciprocals
 secondaries = blaster.find_secondaries

data/lib/crb-blast.rb

@@ -3,7 +3,7 @@
 require 'bio'
 require 'which'
 require 'hit'
-require 'crb-blast'
+require 'threach'
 
 class Bio::FastaFormat
   def isNucl?
@@ -119,51 +119,142 @@ class CRB_Blast
     [@query_name, @target_name]
   end
 
-  def run_blast(evalue, threads)
+  def run_blast(evalue, threads, split)
     if @databases
       @output1 = "#{@working_dir}/#{query_name}_into_#{target_name}.1.blast"
       @output2 = "#{@working_dir}/#{target_name}_into_#{query_name}.2.blast"
-      cmd1=""
-      cmd2=""
       if @query_is_prot
         if @target_is_prot
-          cmd1 << "#{@blastp_path} "
-          cmd2 << "#{@blastp_path} "
+          bin1 = "#{@blastp_path} "
+          bin2 = "#{@blastp_path} "
         else
-          cmd1 << "#{@tblastn_path} "
-          cmd2 << "#{@blastx_path} "
+          bin1 = "#{@tblastn_path} "
+          bin2 = "#{@blastx_path} "
         end
       else
         if @target_is_prot
-          cmd1 << "#{@blastx_path} "
-          cmd2 << "#{@tblastn_path} "
+          bin1 = "#{@blastx_path} "
+          bin2 = "#{@tblastn_path} "
         else
-          cmd1 << "#{@blastn_path} "
-          cmd2 << "#{@blastn_path} "
+          bin1 = "#{@blastn_path} "
+          bin2 = "#{@blastn_path} "
         end
       end
-      cmd1 << " -query #{@query} -db #{@working_dir}/#{@target_name} "
-      cmd1 << " -out #{@output1} -evalue #{evalue} "
+      if split and threads > 1
+        run_blast_with_splitting evalue, threads, bin1, bin2
+      else
+        run_blast_with_threads evalue, threads, bin1, bin2
+      end
+      return true
+    else
+      return false
+    end
+  end
+
+  def run_blast_with_threads evalue, threads, bin1, bin2
+    # puts "running blast with #{threads} threads"
+    cmd1 = "#{bin1} -query #{@query} -db #{@working_dir}/#{@target_name} "
+    cmd1 << " -out #{@output1} -evalue #{evalue} "
+    cmd1 << " -outfmt \"6 std qlen slen\" "
+    cmd1 << " -max_target_seqs 50 "
+    cmd1 << " -num_threads #{threads}"
+
+    cmd2 = "#{bin2} -query #{@target} -db #{@working_dir}/#{@query_name} "
+    cmd2 << " -out #{@output2} -evalue #{evalue} "
+    cmd2 << " -outfmt \"6 std qlen slen\" "
+    cmd2 << " -max_target_seqs 50 "
+    cmd2 << " -num_threads #{threads}"
+    if !File.exist?("#{@output1}")
+      `#{cmd1}`
+    end
+
+    if !File.exist?("#{@output2}")
+      `#{cmd2}`
+    end
+  end
+
+  def run_blast_with_splitting evalue, threads, bin1, bin2
+    # puts "running blast by splitting input into #{threads} pieces"
+    blasts=[]
+    files = split_input(@query, threads)
+    files.threach(threads) do |thread|
+      cmd1 = "#{bin1} -query #{thread} -db #{@working_dir}/#{@target_name} "
+      cmd1 << " -out #{thread}.blast -evalue #{evalue} "
       cmd1 << " -outfmt \"6 std qlen slen\" "
       cmd1 << " -max_target_seqs 50 "
-      cmd1 << " -num_threads #{threads}"
+      cmd1 << " -num_threads 1"
+      if !File.exists?("#{thread}.blast")
+        `#{cmd1}`
+      end
+      blasts << "#{thread}.blast"
+    end
+    cat_cmd = "cat "
+    cat_cmd << blasts.join(" ")
+    cat_cmd << " > #{@output1}"
+    `#{cat_cmd}`
+    blasts.each do |b|
+      File.delete(b) # delete intermediate blast output files
+    end
 
-      cmd2 << " -query #{@target} -db #{@working_dir}/#{@query_name} "
-      cmd2 << " -out #{@output2} -evalue #{evalue} "
+    blasts=[]
+    files = split_input(@target, threads)
+    files.threach(threads) do |thread|
+      cmd2 = "#{bin2} -query #{thread} -db #{@working_dir}/#{@query_name} "
+      cmd2 << " -out #{thread}.blast -evalue #{evalue} "
       cmd2 << " -outfmt \"6 std qlen slen\" "
       cmd2 << " -max_target_seqs 50 "
-      cmd2 << " -num_threads #{threads}"
-
-      if !File.exists?("#{@output1}")
-        `#{cmd1}`
-      end
-      if !File.exists?("#{@output2}")
+      cmd2 << " -num_threads 1"
+      if !File.exists?("#{thread}.blast")
         `#{cmd2}`
       end
-      return true
-    else
-      return false
+      blasts << "#{thread}.blast"
+    end
+    cat_cmd = "cat "
+    cat_cmd << blasts.join(" ")
+    cat_cmd << " > #{@output2}"
+    `#{cat_cmd}`
+    blasts.each do |b|
+      File.delete(b) # delete intermediate blast output files
+    end
+
+  end
+
+  def split_input filename, pieces
+    input = {}
+    name = nil
+    seq=""
+    File.open(filename).each_line do |line|
+      if line =~ /^>(.*)$/
+        if name
+          input[name]=seq
+          seq=""
+        end
+        name = $1
+      else
+        seq << line.chomp
+      end
+    end
+    input[name]=seq
+    # construct list of output file handles
+    outputs=[]
+    output_files=[]
+    pieces.times do |n|
+      outfile = "#{filename}_chunk_#{n}.fasta"
+      outputs[n] = File.open("#{outfile}", "w")
+      output_files[n] = "#{outfile}"
+    end
+    # write sequences
+    count=0
+    input.each_pair do |name, seq|
+      outputs[count].write(">#{name}\n")
+      outputs[count].write("#{seq}\n")
+      count += 1
+      count %= pieces
+    end
+    outputs.each do |out|
+      out.close
     end
+    output_files
   end
 
   def load_outputs
@@ -312,9 +403,9 @@ class CRB_Blast
     @target_results = nil
   end
 
-  def run evalue, threads
+  def run evalue, threads, split
     makedb
-    run_blast evalue, threads
+    run_blast evalue, threads, split
     load_outputs
     find_reciprocals
     find_secondaries

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: crb-blast
 version: !ruby/object:Gem::Version
-  version: '0.2'
+  version: '0.3'
 platform: ruby
 authors:
 - Chris Boursnell
@@ -15,48 +15,48 @@ dependencies:
   name: trollop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.3
 - !ruby/object:Gem::Dependency
@@ -73,60 +73,94 @@ dependencies:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.0.2
+- !ruby/object:Gem::Dependency
+  name: threach
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: bindeps
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.7
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.7
 - !ruby/object:Gem::Dependency
   name: turn
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: shoulda-context
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.6.7
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.6.7
 description: See summary
@@ -136,9 +170,9 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- bin/crb-blast
 - lib/crb-blast.rb
 - lib/hit.rb
-- bin/crb-blast
 homepage: http://rubygems.org/gems/crb-blast
 licenses:
 - MIT
@@ -149,19 +183,18 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.6
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Run conditional reciprocal best blast
 test_files: []
-has_rdoc: