Class: String

Inherits:
Object show all
Includes:
RGFA::FieldParser, RGFA::FieldValidator, RGFA::Sequence
Defined in:
lib/rgfa.rb,
lib/rgfa/line.rb,
lib/rgfa/cigar.rb,
lib/rgfa/sequence.rb,
lib/rgfa/byte_array.rb,
lib/rgfa/field_parser.rb,
lib/rgfa/numeric_array.rb,
lib/rgfa/field_validator.rb

Overview

Method to create a numeric array from a string

Constant Summary

Constants included from RGFA::FieldValidator

RGFA::FieldValidator::DATASTRING_VALIDATION_REGEXP

Constants included from RGFA::Sequence

RGFA::Sequence::WCC

Instance Method Summary collapse

Methods included from RGFA::FieldValidator

#validate_gfa_field!

Methods included from RGFA::FieldParser

#parse_gfa_field, #parse_gfa_optfield

Methods included from RGFA::Sequence

#rc

Instance Method Details

#to_byte_array ⇒ RGFA::ByteArray

Convert a GFA string representation of a byte array to a byte array

Returns:

Raises:



66
67
68
69
70
71
72
73
 
# File 'lib/rgfa/byte_array.rb', line 66

def to_byte_array
  if (size < 2) or (size % 2 == 1)
    raise RGFA::ByteArray::FormatError,
      "Invalid byte array string #{self}; "+
      "each element must be represented by two letters [0-9A-F]"
  end
  scan(/..?/).map {|x|Integer(x,16)}.to_byte_array
end

#to_cigar ⇒ RGFA::CIGAR

Parse CIGAR string and return an array of CIGAR operations

Returns:

  • (RGFA::CIGAR) —

    CIGAR operations (empty if string is “*”)

Raises:



153
154
155
 
# File 'lib/rgfa/cigar.rb', line 153

def to_cigar
  RGFA::CIGAR.from_string(self)
end

#to_numeric_array(validate: true) ⇒ RGFA::NumericArray

Create a numeric array from a string

Parameters:

  • validate (Boolean) (defaults to: true) —

    (default: true) if true, validate the range of the numeric values, according to the array subtype

Returns:

Raises:



167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
 
# File 'lib/rgfa/numeric_array.rb', line 167

def to_numeric_array(validate: true)
  elems = split(",")
  subtype = elems.shift
  integer = (subtype != "f")
  if integer
    range = RGFA::NumericArray::SUBTYPE_RANGE[subtype]
  elsif !RGFA::NumericArray::SUBTYPE.include?(subtype)
    raise RGFA::NumericArray::TypeError, "Subtype #{subtype} unknown"
  end
  elems.map do |e|
    begin
      if integer
        e = Integer(e)
        if validate and not range.include?(e)
          raise "NumericArray: "+
                "value is outside of subtype #{subtype} range\n"+
                "Value: #{e}\n"+
                "Range: #{range.inspect}\n"+
                "Content: #{inspect}"
        end
        e
      else
        Float(e)
      end
    rescue => msg
      raise RGFA::NumericArray::ValueError, msg
    end
  end
end

#to_rgfa(validate: 2) ⇒ RGFA

Converts a String into a RGFA instance. Each line of the string is added separately to the gfa.

Parameters:

  • validate (Integer) (defaults to: 2) —

    (defaults to: 2) the validation level; see “Validation level” under RGFA::Line#initialize.

Returns:



353
354
355
356
357
358
 
# File 'lib/rgfa.rb', line 353

def to_rgfa(validate: 2)
  gfa = RGFA.new(validate: validate)
  split("\n").each {|line| gfa << line}
  gfa.validate! if validate >= 1
  return gfa
end

#to_rgfa_line(validate: 2) ⇒ subclass of RGFA::Line

Parses a line of a RGFA file and creates an object of the correct

record type child class of {RGFA::Line}

Parameters:

  • validate (Integer) (defaults to: 2) —

    (defaults to: 2) see RGFA::Line#initialize

Returns:

Raises:

  • (RGFA::Error) —

    if the fields do not comply to the RGFA specification



698
699
700
 
# File 'lib/rgfa/line.rb', line 698

def to_rgfa_line(validate: 2)
  split(RGFA::Line::SEPARATOR).to_rgfa_line(validate: validate)
end