bio-gadget 0.2.6 → 0.3.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 9bd8ea9d5f88557147da247ea9f817d4f069aae1
+  data.tar.gz: 60235e4a8b6b82c01366d27f38bd4c40e0ef0e71
+SHA512:
+  metadata.gz: bdb115e0f1e9df39a39e108e7f8d00e9a1f2d69ed51b098217659050291034e5a052eaa2aed976cf6b9d18bea5a5929149367fe6b0f33e9a0ee7bc245668d2a5
+  data.tar.gz: d959b569cec30289b3bdf16676b4b26a5e0ed7adceb3e90407646ba074b5621d506eae98f362d57e4b838525d370fc91112e88141dea24a6ae4da3b2dc8faa80

data/README.org

@@ -10,18 +10,18 @@
 
 To check all commands in this package,
 
-: gthor help bio
-: gthor list bio
+: bio-gadget help
+: bio-gadget list
 
 Currently available commands are
 
 : bio
 : ---
-: gthor bio:dedup          # deduplicate fastq (via STDIN)
-: gthor bio:demlt BC POS   # demultiplex fastq (via STDIN) by barcodes
-: gthor bio:fqxz           # 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
+: bio-gadget dedup                                # deduplicate fastq (via STDIN)
+: bio-gadget demlt -b,--barcode-file=BARCODE-FILE # demultiplex fastq by barcodes
+: bio-gadget fqxz                                 # automatic (re)compression of *.fq(.gz|.bz2) files
+: bio-gadget qvstat QUAL                          # statistics of quality values in *.qual file
+: bio-gadget wigchr WIG CHR                       # extract wiggle track on specified chromosome
 
 * Contributing
 

data/bin/bio-gadget

@@ -0,0 +1,5 @@
+#!/usr/bin/env ruby
+
+require 'bio-gadget'
+
+Bio::Gadget.start

data/bio-gadget.gemspec

@@ -14,7 +14,7 @@ Gem::Specification.new do |gem|
   gem.require_paths = ["lib"]
   gem.version       = Bio::Gadget::VERSION
 
-  gem.add_dependency 'gthor'
+  gem.add_dependency 'thor'
   gem.add_dependency 'parallel'
   gem.add_dependency 'levenshtein-ffi'
   gem.add_dependency 'bio-faster'

data/lib/bio-gadget/demlt.rb

@@ -5,14 +5,19 @@ require 'parallel'
 
 module Bio
   class Gadget < Thor
+
     namespace :bio
 
-    desc 'demlt BC POS LEN', 'demultiplex fastq (via STDIN) by barcodes'
-    option 'output-dir', :aliases => '-o', :type => :string, :default  => '.'
-    def demlt(bcfile, tmpofs, tmplen)
+    desc 'demlt', 'demultiplex fastq from STDIN by barcodes'
+    option 'barcode-file', :aliases => '-b', :type => :string, :required => true
+    option 'output-dir', :aliases => '-o', :type => :string, :default => '.'
+    option 'umi-length', :aliases => '-u', :type => :numeric, :default => 4
+    option 'cdna-length', :aliases => '-c', :type => :numeric, :default => 37
+    def demlt
 
-      ofs = tmpofs.to_i
-      len = tmplen.to_i
+      bcfile = options['barcode-file']
+      ofs = options['umi-length']
+      len = options['cdna-length']
 
       wells = Array.new
       bcs = Array.new

data/lib/bio-gadget/version.rb

@@ -3,7 +3,7 @@ require 'thor'
 module Bio
   class Gadget < Thor
 
-    VERSION = "0.2.6"
+    VERSION = "0.3.0"
 
   end
 end

metadata

@@ -1,100 +1,90 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.2.6
-  prerelease: 
+  version: 0.3.0
 platform: ruby
 authors:
 - Shintaro Katayama
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-25 00:00:00.000000000 Z
+date: 2013-03-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: gthor
+  name: thor
   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: 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'
 - !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'
 - !ruby/object:Gem::Dependency
   name: mkfifo
   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
-executables: []
+executables:
+- bio-gadget
 extensions: []
 extra_rdoc_files: []
 files:
@@ -104,6 +94,7 @@ files:
 - LICENSE
 - README.org
 - Rakefile
+- bin/bio-gadget
 - bio-gadget.gemspec
 - lib/bio-gadget.rb
 - lib/bio-gadget/dedup.rb
@@ -114,26 +105,25 @@ files:
 - lib/bio-gadget/wigchr.rb
 homepage: https://github.com/shka/ruby-bio-gadget
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.0.0
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Gadgets for bioinformatics
 test_files: []