bio-gff3-pltools 0.2.0 → 0.3.0

data/README.md

@@ -56,7 +56,7 @@ require the library:
 
 The API docs are online:
 
-  http://mamarjan.github.com/bioruby-gff3-pltools/docs/0.2.0/ruby-api/ 
+  http://mamarjan.github.com/gff3-pltools/docs/0.3.0/ruby-api/ 
 
 For more code examples see the test files in the source tree.
 
@@ -64,7 +64,7 @@ For more code examples see the test files in the source tree.
 
 Project home page can be found at the following location:
 
-  http://mamarjan.github.com/bioruby-gff3-pltools/
+  http://mamarjan.github.com/gff3-pltools/
 
 For information on the source tree, issues and
 how to contribute, see

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.3.0

data/lib/bio-gff3-pltools/filtering.rb

@@ -3,7 +3,8 @@ module Bio
     module GFF3
       # Runs the gff3-ffetch utility with the specified parameters on
       # an external file. Options include :output, :at_most,
-      # :pass_fasta_through, :keep_comments, :keep_pragmas
+      # :keep_fasta, :keep_comments, :keep_pragmas, :gtf_output,
+      # :json_output, :select
       def self.filter_file filename, filter_string, options = {}
         if !File.exists?(filename)
           raise Exception.new("No such file - #{filename}")
@@ -17,8 +18,8 @@ module Bio
         if !options[:at_most].nil?
           at_most_option = "--at-most #{options[:at_most]}"
         end
-        if options[:pass_fasta_through]
-          fasta_option = "--pass-fasta-through"
+        if options[:keep_fasta]
+          fasta_option = "--keep-fasta"
         end
         if options[:keep_comments]
           comments_option = "--keep-comments"
@@ -26,7 +27,17 @@ module Bio
         if options[:keep_pragmas]
           pragmas_option = "--keep-pragmas"
         end
-        gff3_ffetch = IO.popen("gff3-ffetch --filter #{filter_string} #{filename} #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option}")
+        if options[:gtf_output]
+          gtf_output_option = "--gtf-output"
+        end
+        if options[:json_output]
+          json_output_option = "--json"
+        end
+        if !options[:select].nil?
+          select_option = "--select \"#{options[:select]}\""
+        end
+        puts "gff3-ffetch --filter \"#{filter_string}\" #{filename} #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option} #{gtf_output_option} #{json_output_option} #{select_option}"
+        gff3_ffetch = IO.popen("gff3-ffetch --filter \"#{filter_string}\" #{filename} #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option} #{gtf_output_option} #{json_output_option} #{select_option}")
         if output_option.nil?
           output = gff3_ffetch.read
         end
@@ -36,7 +47,8 @@ module Bio
 
       # Runs the gff3-ffetch utility with the specified parameters while
       # passing data to its stdin. Options include :output and :at_most,
-      # :pass_fasta_through, :keep_comments, :keep_pragmas
+      # :keep_fasta, :keep_comments, :keep_pragmas, :gtf_output,
+      # :json_output, :select
       def self.filter_data data, filter_string, options = {}
         output_option = nil
         output = nil
@@ -46,8 +58,8 @@ module Bio
         if !options[:at_most].nil?
           at_most_option = "--at-most #{options[:at_most]}"
         end
-        if options[:pass_fasta_through]
-          fasta_option = "--pass-fasta-through"
+        if options[:keep_fasta]
+          fasta_option = "--keep-fasta"
         end
         if options[:keep_comments]
           comments_option = "--keep-comments"
@@ -55,7 +67,16 @@ module Bio
         if options[:keep_pragmas]
           pragmas_option = "--keep-pragmas"
         end
-        gff3_ffetch = IO.popen("gff3-ffetch --filter #{filter_string} - #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option}", "r+")
+        if options[:gtf_output]
+          gtf_output_option = "--gtf-output"
+        end
+        if options[:json_output]
+          json_output_option = "--json"
+        end
+        if !options[:select].nil?
+          select_option = "--select \"#{options[:select]}\""
+        end
+        gff3_ffetch = IO.popen("gff3-ffetch --filter \"#{filter_string}\" - #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option} #{gtf_output_option} #{json_output_option} #{select_option}", "r+")
         gff3_ffetch.write data
         gff3_ffetch.close_write
         if output_option.nil?
@@ -65,6 +86,92 @@ module Bio
         output
       end
     end
+
+    module GTF
+      # Runs the gtf-ffetch utility with the specified parameters on
+      # an external file. Options include :output, :at_most,
+      # :keep_fasta, :keep_comments, :keep_pragmas, :gff3_output,
+      # :json_output, :select
+      def self.filter_file filename, filter_string, options = {}
+        if !File.exists?(filename)
+          raise Exception.new("No such file - #{filename}")
+        end
+
+        output_option = nil
+        output = nil
+        if !options[:output].nil?
+          output_option = "--output #{options[:output]}"
+        end
+        if !options[:at_most].nil?
+          at_most_option = "--at-most #{options[:at_most]}"
+        end
+        if options[:keep_fasta]
+          fasta_option = "--keep-fasta"
+        end
+        if options[:keep_comments]
+          comments_option = "--keep-comments"
+        end
+        if options[:keep_pragmas]
+          pragmas_option = "--keep-pragmas"
+        end
+        if options[:gff3_output]
+          gff3_output_option = "--gff3-output"
+        end
+        if options[:json_output]
+          json_output_option = "--json"
+        end
+        if !options[:select].nil?
+          select_option = "--select \"#{options[:select]}\""
+        end
+        gff3_ffetch = IO.popen("gtf-ffetch --filter \"#{filter_string}\" #{filename} #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option} #{gff3_output_option} #{json_output_option} #{select_option}")
+        if output_option.nil?
+          output = gtf_ffetch.read
+        end
+        gtf_ffetch.close
+        output
+      end
+
+      # Runs the gtf-ffetch utility with the specified parameters while
+      # passing data to its stdin. Options include :output and :at_most,
+      # :keep_fasta, :keep_comments, :keep_pragmas, :gff3_output,
+      # :json_output, :select
+      def self.filter_data data, filter_string, options = {}
+        output_option = nil
+        output = nil
+        if !options[:output].nil?
+          output_option = "--output #{options[:output]}"
+        end
+        if !options[:at_most].nil?
+          at_most_option = "--at-most #{options[:at_most]}"
+        end
+        if options[:keep_fasta]
+          fasta_option = "--keep-fasta"
+        end
+        if options[:keep_comments]
+          comments_option = "--keep-comments"
+        end
+        if options[:keep_pragmas]
+          pragmas_option = "--keep-pragmas"
+        end
+        if options[:gff3_output]
+          gff3_output_option = "--gff3-output"
+        end
+        if options[:json_output]
+          json_output_option = "--json"
+        end
+        if !options[:select].nil?
+          select_option = "--select \"#{options[:select]}\""
+        end
+        gtf_ffetch = IO.popen("gtf-ffetch --filter \"#{filter_string}\" - #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option} #{gff3_output_option} #{json_output_option} #{select_option}", "r+")
+        gtf_ffetch.write data
+        gtf_ffetch.close_write
+        if output_option.nil?
+          output = gtf_ffetch.read
+        end
+        gtf_ffetch.close
+        output
+      end
+    end
   end
 end
 

data/lib/bio-gff3-pltools/validation.rb

@@ -1,6 +1,9 @@
 module Bio
   module PL
     module GFF3
+      # Runs the gff3-validate utility with the specified filename
+      # as argument. Returns error messages if the utility found
+      # issues in the file.
       def self.validate_file filename
         if !File.exists?(filename)
           raise Exception.new("No such file - #{filename}")

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gff3-pltools
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-14 00:00:00.000000000 Z
+date: 2012-08-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
@@ -168,7 +168,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1031554001
+      hash: -1046642193
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: