Class: Bio::FinishM::ReadInput

Inherits:
Object
  • Object
show all
Defined in:
lib/assembly/read_input.rb

Overview

A class representing reads or sets of reads to be assembled

Constant Summary collapse

READ_INPUT_SYMBOLS = 
[
:fasta_singles, :fastq_singles, :fasta_singles_gz, :fastq_singles_gz,
:interleaved_fasta, :interleaved_fastq, :interleaved_fasta_gz, :interleaved_fastq_gz,
:separate_fasta, :separate_fastq, :separate_fasta_gz, :separate_fastq_gz,
]

Instance Method Summary collapse

Instance Method Details

#add_options(option_parser, options) ⇒ Object

Given an OptionParser, add options to it, which parse out read-related options



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# File 'lib/assembly/read_input.rb', line 13

def add_options(option_parser, options)
  {
    '--fasta' => :fasta_singles,
    '--fastq' => :fastq_singles,
    '--fasta-gz' => :fasta_singles_gz,
    '--fastq-gz' => :fastq_singles_gz,
    '--interleaved-fasta' => :interleaved_fasta,
    '--interleaved-fastq' => :interleaved_fastq,
    '--interleaved-fasta-gz' => :interleaved_fasta_gz,
    '--interleaved-fastq-gz' => :interleaved_fastq_gz,
    '--separate-fasta' => :separate_fasta,
    '--separate-fastq' => :separate_fastq,
    '--separate-fasta-gz' => :separate_fasta_gz,
    '--separate-fastq-gz' => :separate_fastq_gz,
    }.each do |flag, sym|
      option_parser.on("#{flag} PATH", Array, "One or more paths to reads, comma separated") do |arg|
        options[sym] = arg
      end
    end
end

#parse_options(options) ⇒ Object

Parse options from options hash into instance variables for this object



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# File 'lib/assembly/read_input.rb', line 44

def parse_options(options)
  READ_INPUT_SYMBOLS.each do |sym|
    send("#{sym}=",options[sym]) if options[sym]
  end
end

#validate_options(options, argv) ⇒ Object

Require at least 1 set of reads to be given, of any type



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# File 'lib/assembly/read_input.rb', line 35

def validate_options(options, argv)
  return nil if options[:previous_assembly] #bit of a hack, but hey
  READ_INPUT_SYMBOLS.each do |sym|
    return nil if options[sym]
  end
  return "No definition of reads for assembly was found"
end

#velvet_read_arguments ⇒ Object

Output a string to be used on the command line with velvet



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# File 'lib/assembly/read_input.rb', line 51

def velvet_read_arguments
  readset_index = 1
  args = ''
  # Have to put probe sequences (which are single-ended) first in this (ordered) hash
  {
    :fasta_singles => '-fasta -short',
    :fastq_singles => '-fastq -short',
    :fasta_singles_gz => '-fasta.gz -short',
    :fastq_singles_gz => '-fastq.gz -short',
    :interleaved_fasta => '-fasta -shortPaired',
    :interleaved_fastq => '-fastq -shortPaired',
    :interleaved_fasta_gz => '-fasta.gz -shortPaired',
    :interleaved_fastq_gz => '-fastq.gz -shortPaired',
    :separate_fasta => '-fasta -shortPaired -separate',
    :separate_fastq => '-fastq -shortPaired -separate',
    :separate_fasta_gz => '-fasta.gz -shortPaired -separate',
    :separate_fastq_gz => '-fastq.gz -shortPaired -separate',
    }.each do |sym, velvet_flag|
      paths = send(sym)
      unless paths.nil? or paths.empty?
        args += " #{velvet_flag}"
        paths.each do |path|
          args += " #{path}"
        end
      end
    end
  return args
end