bio-gff3-pltools 0.2.0 → 0.3.0

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Files changed (5) hide show
  1. data/README.md +2 -2
  2. data/VERSION +1 -1
  3. data/lib/bio-gff3-pltools/filtering.rb +115 -8
  4. data/lib/bio-gff3-pltools/validation.rb +3 -0
  5. metadata +3 -3
data/README.md CHANGED
@@ -56,7 +56,7 @@ require the library:
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  The API docs are online:
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- http://mamarjan.github.com/bioruby-gff3-pltools/docs/0.2.0/ruby-api/
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+ http://mamarjan.github.com/gff3-pltools/docs/0.3.0/ruby-api/
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  For more code examples see the test files in the source tree.
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@@ -64,7 +64,7 @@ For more code examples see the test files in the source tree.
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  Project home page can be found at the following location:
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- http://mamarjan.github.com/bioruby-gff3-pltools/
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+ http://mamarjan.github.com/gff3-pltools/
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  For information on the source tree, issues and
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  how to contribute, see
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.2.0
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+ 0.3.0
data/lib/bio-gff3-pltools/filtering.rb CHANGED
@@ -3,7 +3,8 @@ module Bio
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  module GFF3
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  # Runs the gff3-ffetch utility with the specified parameters on
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  # an external file. Options include :output, :at_most,
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- # :pass_fasta_through, :keep_comments, :keep_pragmas
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+ # :keep_fasta, :keep_comments, :keep_pragmas, :gtf_output,
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+ # :json_output, :select
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  def self.filter_file filename, filter_string, options = {}
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  if !File.exists?(filename)
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  raise Exception.new("No such file - #{filename}")
@@ -17,8 +18,8 @@ module Bio
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  if !options[:at_most].nil?
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  at_most_option = "--at-most #{options[:at_most]}"
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  end
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- if options[:pass_fasta_through]
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- fasta_option = "--pass-fasta-through"
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+ if options[:keep_fasta]
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+ fasta_option = "--keep-fasta"
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  end
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  if options[:keep_comments]
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  comments_option = "--keep-comments"
@@ -26,7 +27,17 @@ module Bio
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  if options[:keep_pragmas]
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  pragmas_option = "--keep-pragmas"
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  end
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- gff3_ffetch = IO.popen("gff3-ffetch --filter #{filter_string} #{filename} #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option}")
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+ if options[:gtf_output]
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+ gtf_output_option = "--gtf-output"
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+ end
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+ if options[:json_output]
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+ json_output_option = "--json"
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+ end
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+ if !options[:select].nil?
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+ select_option = "--select \"#{options[:select]}\""
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+ end
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+ 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}"
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+ 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}")
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  if output_option.nil?
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  output = gff3_ffetch.read
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  end
@@ -36,7 +47,8 @@ module Bio
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  # Runs the gff3-ffetch utility with the specified parameters while
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  # passing data to its stdin. Options include :output and :at_most,
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- # :pass_fasta_through, :keep_comments, :keep_pragmas
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+ # :keep_fasta, :keep_comments, :keep_pragmas, :gtf_output,
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+ # :json_output, :select
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  def self.filter_data data, filter_string, options = {}
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  output_option = nil
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  output = nil
@@ -46,8 +58,8 @@ module Bio
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  if !options[:at_most].nil?
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  at_most_option = "--at-most #{options[:at_most]}"
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  end
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- if options[:pass_fasta_through]
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- fasta_option = "--pass-fasta-through"
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+ if options[:keep_fasta]
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+ fasta_option = "--keep-fasta"
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  end
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  if options[:keep_comments]
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  comments_option = "--keep-comments"
@@ -55,7 +67,16 @@ module Bio
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  if options[:keep_pragmas]
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  pragmas_option = "--keep-pragmas"
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  end
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- gff3_ffetch = IO.popen("gff3-ffetch --filter #{filter_string} - #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option}", "r+")
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+ if options[:gtf_output]
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+ gtf_output_option = "--gtf-output"
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+ end
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+ if options[:json_output]
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+ json_output_option = "--json"
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+ end
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+ if !options[:select].nil?
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+ select_option = "--select \"#{options[:select]}\""
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+ end
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+ 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+")
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  gff3_ffetch.write data
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  gff3_ffetch.close_write
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  if output_option.nil?
@@ -65,6 +86,92 @@ module Bio
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  output
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  end
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  end
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+
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+ module GTF
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+ # Runs the gtf-ffetch utility with the specified parameters on
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+ # an external file. Options include :output, :at_most,
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+ # :keep_fasta, :keep_comments, :keep_pragmas, :gff3_output,
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+ # :json_output, :select
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+ def self.filter_file filename, filter_string, options = {}
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+ if !File.exists?(filename)
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+ raise Exception.new("No such file - #{filename}")
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+ end
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+
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+ output_option = nil
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+ output = nil
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+ if !options[:output].nil?
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+ output_option = "--output #{options[:output]}"
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+ end
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+ if !options[:at_most].nil?
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+ at_most_option = "--at-most #{options[:at_most]}"
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+ end
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+ if options[:keep_fasta]
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+ fasta_option = "--keep-fasta"
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+ end
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+ if options[:keep_comments]
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+ comments_option = "--keep-comments"
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+ end
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+ if options[:keep_pragmas]
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+ pragmas_option = "--keep-pragmas"
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+ end
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+ if options[:gff3_output]
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+ gff3_output_option = "--gff3-output"
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+ end
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+ if options[:json_output]
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+ json_output_option = "--json"
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+ end
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+ if !options[:select].nil?
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+ select_option = "--select \"#{options[:select]}\""
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+ end
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+ 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}")
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+ if output_option.nil?
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+ output = gtf_ffetch.read
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+ end
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+ gtf_ffetch.close
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+ output
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+ end
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+
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+ # Runs the gtf-ffetch utility with the specified parameters while
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+ # passing data to its stdin. Options include :output and :at_most,
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+ # :keep_fasta, :keep_comments, :keep_pragmas, :gff3_output,
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+ # :json_output, :select
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+ def self.filter_data data, filter_string, options = {}
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+ output_option = nil
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+ output = nil
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+ if !options[:output].nil?
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+ output_option = "--output #{options[:output]}"
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+ end
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+ if !options[:at_most].nil?
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+ at_most_option = "--at-most #{options[:at_most]}"
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+ end
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+ if options[:keep_fasta]
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+ fasta_option = "--keep-fasta"
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+ end
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+ if options[:keep_comments]
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+ comments_option = "--keep-comments"
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+ end
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+ if options[:keep_pragmas]
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+ pragmas_option = "--keep-pragmas"
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+ end
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+ if options[:gff3_output]
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+ gff3_output_option = "--gff3-output"
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+ end
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+ if options[:json_output]
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+ json_output_option = "--json"
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+ end
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+ if !options[:select].nil?
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+ select_option = "--select \"#{options[:select]}\""
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+ end
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+ 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+")
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+ gtf_ffetch.write data
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+ gtf_ffetch.close_write
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+ if output_option.nil?
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+ output = gtf_ffetch.read
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+ end
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+ gtf_ffetch.close
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+ output
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+ end
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+ end
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  end
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  end
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data/lib/bio-gff3-pltools/validation.rb CHANGED
@@ -1,6 +1,9 @@
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  module Bio
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  module PL
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  module GFF3
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+ # Runs the gff3-validate utility with the specified filename
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+ # as argument. Returns error messages if the utility found
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+ # issues in the file.
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  def self.validate_file filename
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  if !File.exists?(filename)
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  raise Exception.new("No such file - #{filename}")
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-gff3-pltools
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  version: !ruby/object:Gem::Version
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- version: 0.2.0
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+ version: 0.3.0
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  prerelease:
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  platform: ruby
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  authors:
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-07-14 00:00:00.000000000 Z
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+ date: 2012-08-07 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rspec
@@ -168,7 +168,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: -1031554001
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+ hash: -1046642193
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements: