bio-gadget 0.1.2 → 0.1.3

data/README.org

@@ -17,6 +17,7 @@ Currently available commands are
 
 : bio
 : ---
+: gthor bio:demlt BC POS   # demultiplex fastq (via STDIN) by barcodes
 : gthor bio:fqlzma         # automatic (re)compression of *.fq(.gz|.bz2) files
 : gthor bio:qvstat QUAL    # statistics of quality values in *.qual file
 : gthor bio:wigchr WIG CHR # extract wiggle track on specified chromosome

data/bio-gadget.gemspec

@@ -1,4 +1,3 @@
-# -*- encoding: utf-8 -*-
 require File.expand_path('../lib/bio-gadget/version', __FILE__)
 
 Gem::Specification.new do |gem|
@@ -17,4 +16,6 @@ Gem::Specification.new do |gem|
 
   gem.add_dependency 'gthor'
   gem.add_dependency 'parallel'
+  gem.add_dependency 'levenshtein-ffi'
+  gem.add_dependency 'bio-faster'
 end

data/lib/bio-gadget.rb

@@ -1,4 +1,5 @@
 require 'bio-gadget/version'
+require 'bio-gadget/demlt'
 require 'bio-gadget/fqlzma'
 require 'bio-gadget/qvstat'
 require 'bio-gadget/wigchr'

data/lib/bio-gadget/demlt.rb

@@ -0,0 +1,82 @@
+require 'bio-faster'
+require 'levenshtein'
+require 'thread'
+
+module Bio
+  class Gadget < Thor
+    namespace :bio
+
+    desc 'demlt BC POS', 'demultiplex fastq (via STDIN) by barcodes'
+    def demlt(bcfile, tmpofs)
+
+      ofs = tmpofs.to_i
+
+      wells = Array.new
+      bcs = Array.new
+      bclens = Array.new
+      open(bcfile).each do |line|
+        cols = line.rstrip.split
+        wells.push(cols[0])
+        bcs.push(cols[1])
+        bclens.push(cols[1].length)
+      end
+
+      bclens.uniq!
+      if bclens.size != 1
+        raise 'Inconsistent barcode sequences'
+      end
+      bclen = bclens[0]
+
+      ts = Array.new
+      qs = Array.new
+      (wells + ['other']).each { |well|
+        q = Queue.new
+        t = Thread.new(well, q) do |well|
+          fp = open("| gzip -c > #{well}.fq.gz", 'w')
+          while vals = q.shift
+            if vals == ""
+              break
+            else
+              fp.puts(vals)
+            end
+          end
+          fp.close()
+        end
+        qs.push(q)
+        ts.push(t)
+      }
+
+      reads = Array.new(bcs.size+1, 0)
+      tmpdist = Hash.new
+      Bio::Faster.new(:stdin).each_record(:quality => :raw) do |seqid, seq, qvs|
+        seqbc = seq[ofs, bclen]
+        bcs.each_index do |i|
+          tmpdist[i] = Levenshtein.distance(bcs[i], seqbc)
+        end
+        dists = tmpdist.sort { |a, b| a[1] <=> b[1] }
+        if dists[0][1] < dists[1][1] && dists[0][1] < 2
+          idx = dists[0][0]
+          qs[idx].push(">#{seqid}\n#{seq}\n+\n#{qvs}")
+          reads[idx] = reads[idx]+1
+        else
+          qs[-1].push(">#{seqid}\n#{seq}\n+\n#{qvs}")
+          reads[-1] = reads[-1]+1
+        end
+      end
+
+      qs.each { |q| q.push('') }
+      ts.each { |t| t.join }
+
+      total = 0
+      bcs.each_index { |i|
+        r = reads[i]
+        puts "#{bcs[i]}\t#{r}\t#{wells[i]}.fq.gz"
+        total = total+r
+      }
+      puts "Other\t#{reads[-1]}\tother.fq.gz"
+      puts '===='
+      puts "Total\t#{total+reads[-1]}"
+
+    end
+  end
+end

data/lib/bio-gadget/version.rb

@@ -3,7 +3,7 @@ require 'thor'
 module Bio
   class Gadget < Thor
 
-    VERSION = "0.1.2"
+    VERSION = "0.1.3"
 
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-12 00:00:00.000000000 Z
+date: 2012-12-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: gthor
@@ -43,6 +43,38 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: levenshtein-ffi
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio-faster
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Gadgets for bioinformatics
 email:
 - shintaro.katayama@gmail.com
@@ -58,6 +90,7 @@ files:
 - Rakefile
 - bio-gadget.gemspec
 - lib/bio-gadget.rb
+- lib/bio-gadget/demlt.rb
 - lib/bio-gadget/fqlzma.rb
 - lib/bio-gadget/qvstat.rb
 - lib/bio-gadget/version.rb