bio-gadget 0.1.0 → 0.1.1

data/Gthorfile

@@ -1,46 +1,2 @@
-module Bio
-  class Gadget < Thor
-
-    namespace :bio
-
-    desc 'qvstat QUAL', 'statistics of quality values in *.qual file'
-    def qvstat(qualfile)
-      stat = Hash.new
-      myopen(qualfile) { |fp|
-        fp.each { |line|
-          next if /^[\#\>]/ =~ line
-          qvs = line.rstrip.split
-          qvs.each_index { |i|
-            qv = qvs[i]
-            stat[qv] = Array.new unless stat.key?(qv)
-            if stat[qv][i].nil?
-              stat[qv][i] = 1
-            else
-              stat[qv][i] += 1
-            end
-          }
-        }
-      }
-      statfile = qualfile.sub(/.qual(.gz)?$/, '.qvstat')
-      open(statfile, 'w') { |out|
-        qvs = stat.keys.sort { |a, b| a.to_i <=> b.to_i }
-        qvs.each { |qv|
-          out.puts "#{qv} #{stat[qv].join(' ')}"
-        }
-      }
-    end
-
-    private
-
-    def myopen(file, &block)
-      # how to write?
-      f = (/\|/ !~ file && /\.gz$/ =~ file) ? "| gunzip -c #{file}" : file
-      unless block.nil?
-        o = open(f); block.call(o); o.close
-      else
-        open(f)
-      end
-    end
-
-  end
-end
+$:.unshift File.expand_path('../lib', __FILE__)
+require 'bio-gadget'

data/README.org

@@ -8,9 +8,18 @@
 
 * Usage
 
+To check all commands in this package,
+
 : gthor help bio
 : gthor list bio
 
+Currently available commands are
+
+: bio
+: ---
+: gthor bio:fqlzma       # automatic (re)compression of *.fq(.gz|.bz2) files
+: gthor bio:qvstat QUAL  # statistics of quality values in *.qual file
+
 * Contributing
 
 1. Fork it

data/bio-gadget.gemspec

@@ -16,4 +16,5 @@ Gem::Specification.new do |gem|
   gem.version       = Bio::Gadget::VERSION
 
   gem.add_dependency 'gthor'
+  gem.add_dependency 'parallel'
 end

data/lib/bio-gadget.rb

@@ -1,7 +1,3 @@
-require "bio-gadget/version"
-
-module Bio
-  module Gadget
-    # Your code goes here...
-  end
-end
+require 'bio-gadget/version'
+require 'bio-gadget/fqlzma'
+require 'bio-gadget/qvstat'

data/lib/bio-gadget/fqlzma.rb

@@ -0,0 +1,30 @@
+require 'parallel'
+require 'pathname'
+
+module Bio
+  class Gadget < Thor
+
+    namespace :bio
+
+    desc 'fqlzma', 'automatic (re)compression of *.fq(.gz|.bz2) files'
+    def fqlzma
+      Parallel.map(Pathname.glob('*.fq{.gz,.bz2,}')) { |fqfilename|
+        lzmafilename = fqfilename.sub(/\.fq(\.(gz|bz2))*$/, '.fq.lzma')
+        if !lzmafilename.exist?
+          case fqfilename.extname
+          when '.gz'
+            decompressor = 'gunzip -c'
+          when '.bz2'
+            decompressor = 'bunzip2 -c'
+          else
+            decompressor = 'cat'
+          end
+          puts "compressing #{lzmafilename}..."
+          system "#{decompressor} #{fqfilename} | lzma -c > #{lzmafilename} 2> #{lzmafilename}.log"
+          system "lzma -t #{lzmafilename} >> #{lzmafilename}.log 2>&1"
+        end
+      }
+    end
+
+  end
+end

data/lib/bio-gadget/qvstat.rb

@@ -0,0 +1,46 @@
+module Bio
+  class Gadget < Thor
+
+    namespace :bio
+
+    desc 'qvstat QUAL', 'statistics of quality values in *.qual file'
+    def qvstat(qualfile)
+      stat = Hash.new
+      myopen(qualfile) { |fp|
+        fp.each { |line|
+          next if /^[\#\>]/ =~ line
+          qvs = line.rstrip.split
+          qvs.each_index { |i|
+            qv = qvs[i]
+            stat[qv] = Array.new unless stat.key?(qv)
+            if stat[qv][i].nil?
+              stat[qv][i] = 1
+            else
+              stat[qv][i] += 1
+            end
+          }
+        }
+      }
+      statfile = qualfile.sub(/.qual(.gz)?$/, '.qvstat')
+      open(statfile, 'w') { |out|
+        qvs = stat.keys.sort { |a, b| a.to_i <=> b.to_i }
+        qvs.each { |qv|
+          out.puts "#{qv} #{stat[qv].join(' ')}"
+        }
+      }
+    end
+
+    private
+
+    def myopen(file, &block)
+      # how to write?
+      f = (/\|/ !~ file && /\.gz$/ =~ file) ? "| gunzip -c #{file}" : file
+      unless block.nil?
+        o = open(f); block.call(o); o.close
+      else
+        open(f)
+      end
+    end
+
+  end
+end

data/lib/bio-gadget/version.rb

@@ -1,5 +1,9 @@
+require 'thor'
+
 module Bio
-  module Gadget
-    VERSION = "0.1.0"
+  class Gadget < Thor
+
+    VERSION = "0.1.1"
+
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-20 00:00:00.000000000 Z
+date: 2012-10-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: gthor
@@ -27,6 +27,22 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: parallel
+  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
@@ -42,6 +58,8 @@ files:
 - Rakefile
 - bio-gadget.gemspec
 - lib/bio-gadget.rb
+- lib/bio-gadget/fqlzma.rb
+- lib/bio-gadget/qvstat.rb
 - lib/bio-gadget/version.rb
 homepage: https://github.com/shka/ruby-bio-gadget
 licenses: []