Class: Bio::Velvet::CnyUnifiedSeqNamesFile

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-velvet/sequence_names.rb

Overview

Methods for dealing with the CnyUnifiedSeq.names file output when the -create_binary flag is set in velveth.

Class Method Summary collapse

Class Method Details

.extract_entries(path_to_cny_unified_seq_names_file, entry_names) ⇒ Object

Return a hash of seqname => (Array of CnyUnifiedSeqNamesFileEntry objects) created by parsing the CnyUnifiedSeq.names file. Sometimes sequences can be found multiple times e.g. if fwd and rev of a pair is delineated after a space in the input names.



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# File 'lib/bio-velvet/sequence_names.rb', line 14

def self.extract_entries(path_to_cny_unified_seq_names_file, entry_names)
  # Create results hash
  to_return = {}
  entry_names.each do |name|
    to_return[name] = []
  end

  Hopcsv.foreach(path_to_cny_unified_seq_names_file,"\t") do |row|
    name = row[0][1...row[0].length] #remove '>' at the start of the name
    next unless to_return.key?(name) #ignore uninsteresting sequences

    entry = CnyUnifiedSeqNamesFileEntry.new
    entry.name = name
    entry.read_id = row[1].to_i
    entry.category = row[2].to_i
    to_return[name].push entry
  end
  return to_return
end

.extract_entries_using_grep_hack(path_to_cny_unified_seq_names_file, entry_names) ⇒ Object

These files can be quite big, so this method



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# File 'lib/bio-velvet/sequence_names.rb', line 35

def self.extract_entries_using_grep_hack(path_to_cny_unified_seq_names_file, entry_names)
  to_return = nil
  Tempfile.open('velvet_names_grep_hack_in') do |input|
    entry_names.each do |name|
      input.puts ">#{name}\t"
    end
    input.close #flush

    Tempfile.open('velvet_names_grep_hack_result') do |output|
      Bio::Commandeer.run "grep -F -f #{input.path} #{path_to_cny_unified_seq_names_file.inspect} >#{output.path}"
      to_return = extract_entries output.path, entry_names
    end
  end
  return to_return
end