bio-gadget 0.1.1 → 0.1.2

data/README.org

@@ -17,13 +17,16 @@ 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
+: 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
 
 * Contributing
 
 1. Fork it
 2. Create your feature branch (`git checkout -b my-new-feature`)
-3. Commit your changes (`git commit -am 'Added some feature'`)
-4. Push to the branch (`git push origin my-new-feature`)
-5. Create new Pull Request
+3. (optional) Install gems (`bundle`)
+4. Add your feature
+5. Commit your changes (`git commit -am 'Added some feature'`)
+6. Push to the branch (`git push origin my-new-feature`)
+7. Create new Pull Request

data/lib/bio-gadget.rb

@@ -1,3 +1,24 @@
 require 'bio-gadget/version'
 require 'bio-gadget/fqlzma'
 require 'bio-gadget/qvstat'
+require 'bio-gadget/wigchr'
+
+module Bio
+  class Gadget < Thor
+
+    namespace :bio
+
+    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/qvstat.rb

@@ -30,17 +30,5 @@ module Bio
       }
     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

@@ -3,7 +3,7 @@ require 'thor'
 module Bio
   class Gadget < Thor
 
-    VERSION = "0.1.1"
+    VERSION = "0.1.2"
 
   end
 end

data/lib/bio-gadget/wigchr.rb

@@ -0,0 +1,28 @@
+module Bio
+  class Gadget < Thor
+
+    namespace :bio
+
+    desc 'wigchr WIG CHR', 'extract wiggle track on specified chromosome'
+    def wigchr(wigfile, chr)
+      target = false
+      myopen(wigfile) { |fp|
+        fp.each { |line|
+          if (/^(fixed|variable)Step/ =~ line)
+            if (/chrom=#{chr}\s/ =~ line)
+              target = true
+              puts line
+            else
+              target = false
+            end
+          elsif (/^\d/ =~ line)
+            puts line if target
+          else
+            puts line
+          end
+        }
+      }
+    end
+
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gadget
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-10-14 00:00:00.000000000 Z
+date: 2012-11-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: gthor
@@ -61,6 +61,7 @@ files:
 - lib/bio-gadget/fqlzma.rb
 - lib/bio-gadget/qvstat.rb
 - lib/bio-gadget/version.rb
+- lib/bio-gadget/wigchr.rb
 homepage: https://github.com/shka/ruby-bio-gadget
 licenses: []
 post_install_message: