class Bio::GFF::GFF2::Record

Stores GFF2 record.

Attributes

comment[RW]

Comment for the GFF record

Public Class Methods

new(*arg) click to toggle source

Creates a Bio::GFF::GFF2::Record object. Is typically not called directly, but is called automatically when creating a Bio::GFF::GFF2 object.

Arguments:

str: a tab-delimited line in GFF2 format

Arguments:

seqname: seqname (String or nil)
source: source (String or nil)
feature: feature type (String)
start_position: start (Integer)
end_position: end (Integer)
score: score (Float or nil)
strand: strand (String or nil)
frame: frame (Integer or nil)
attributes: attributes (Array or nil)

# File lib/bio/db/gff.rb, line 381
def initialize(*arg)
  if arg.size == 1 then
    parse(arg[0])
  else
    @seqname, @source, @feature,
    start, endp, @score, @strand, frame,
    @attributes = arg
    @start = start ? start.to_i : nil
    @end   = endp  ? endp.to_i : nil
    @score = score ? score.to_f : nil
    @frame = frame ? frame.to_i : nil
  end
  @attributes ||= []
end

parse(str) click to toggle source

Parses a GFF2-formatted line and returns a new Bio::GFF::GFF2::Record object.

# File lib/bio/db/gff.rb, line 360
def self.parse(str)
  self.new.parse(str)
end

Public Instance Methods

==(other) click to toggle source

Returns true if self == other. Otherwise, returns false.

Calls superclass method

# File lib/bio/db/gff.rb, line 478
def ==(other)
  super ||
    ((self.class == other.class and
      self.seqname == other.seqname and
      self.source  == other.source and
      self.feature == other.feature and
      self.start   == other.start and
      self.end     == other.end and
      self.score   == other.score and
      self.strand  == other.strand and
      self.frame   == other.frame and
      self.attributes == other.attributes) ? true : false)
end

add_attribute(tag, value) click to toggle source

Adds a new tag-value pair.

Arguments:

(required) tag: String
(required) value: String or Bio::GFF::GFF2::Record::Value object.

Returns: value

# File lib/bio/db/gff.rb, line 582
def add_attribute(tag, value)
  @attributes.push([ String.new(tag), value ])
end

attribute(tag)

Alias for: get_attribute

attributes_to_hash() click to toggle source

Returns hash representation of attributes.

Note: If two or more tag-value pairs with same tag names exist, only the first tag-value pair is used for each tag.

Returns: Hash object

# File lib/bio/db/gff.rb, line 660
def attributes_to_hash
  h = {}
  @attributes.each do |x|
    key, val = x
    h[key] = val unless h[key]
  end
  h
end

comment_only?() click to toggle source

Returns true if the entry is empty except for comment. Otherwise, returns false.

# File lib/bio/db/gff.rb, line 438
def comment_only?
  if !@seqname and
      !@source and
      !@feature and
      !@start and
      !@end and
      !@score and
      !@strand and
      !@frame and
      @attributes.empty? then
    true
  else
    false
  end
end

comments() click to toggle source

“comments” is deprecated. Instead, use “comment”.

# File lib/bio/db/gff.rb, line 400
def comments
  warn "#{self.class.to_s}#comments is deprecated. Instead, use \"comment\"."
  self.comment
end

comments=(str) click to toggle source

“comments=” is deprecated. Instead, use “comment=”.

# File lib/bio/db/gff.rb, line 406
def comments=(str)
  warn "#{self.class.to_s}#comments= is deprecated. Instead, use \"comment=\"."
  self.comment = str
end

delete_attribute(tag, value) click to toggle source

Removes a specific tag-value pair.

Note that if two or more tag-value pairs found, only the first tag-value pair is removed.

Arguments:

(required) tag: String
(required) value: String or Bio::GFF::GFF2::Record::Value object.

Returns: if removed, value. Otherwise, nil.

# File lib/bio/db/gff.rb, line 596
def delete_attribute(tag, value)
  removed = nil
  if i = @attributes.index([ tag, value ]) then
    ary = @attributes.delete_at(i)
    removed = ary[1]
  end
  removed
end

delete_attributes(tag) click to toggle source

Removes all attributes with the specified tag.

Arguments:

(required) tag: String

Returns: if removed, self. Otherwise, nil.

# File lib/bio/db/gff.rb, line 611
def delete_attributes(tag)
  @attributes.reject! do |x|
    x[0] == tag
  end ? self : nil
end

get_attribute(tag) click to toggle source

Gets the attribute value for the given tag.

Note that if two or more tag-value pairs with the same name found, only the first value is returned.

Arguments:

(required) tag: String

Returns: String, Bio::GFF::GFF2::Record::Value object, or nil.

# File lib/bio/db/gff.rb, line 500
def get_attribute(tag)
  ary = @attributes.assoc(tag)
  ary ? ary[1] : nil
end

Also aliased as: attribute

get_attributes(tag) click to toggle source

Gets the attribute values for the given tag. This method always returns an array.

Arguments:

(required) tag: String

Returns: Array containing String or \

Bio::GFF::GFF2::Record::Value objects.

# File lib/bio/db/gff.rb, line 513
def get_attributes(tag)
  ary = @attributes.find_all do |x|
    x[0] == tag
  end
  ary.collect! { |x| x[1] }
  ary
end

parse(string) click to toggle source

Parses a GFF2-formatted line and stores data from the string. Note that all existing data is wiped out.

# File lib/bio/db/gff.rb, line 413
def parse(string)
  if /^\s*\#/ =~ string then
    @comment = string[/\#(.*)/, 1].chomp
    columns = []
  else
    columns = string.chomp.split("\t", 10)
    @comment = columns[9][/\#(.*)/, 1].chomp if columns[9]
  end

  @seqname, @source, @feature,
  start, endp, score, @strand, frame =
    columns[0, 8].collect { |x|
    str = unescape(x)
    str == '.' ? nil : str
  }
  @start = start ? start.to_i : nil
  @end   = endp  ? endp.to_i : nil
  @score = score ? score.to_f : nil
  @frame = frame ? frame.to_i : nil

  @attributes = parse_attributes(columns[8])
end

replace_attributes(tag, *values) click to toggle source

Replaces values for the given tags with new values. Existing values for the tag are completely wiped out and replaced by new tag-value pairs. If the tag does not exist, the tag-value pairs are newly added.

Arguments:

(required) tag: String
(required) values: String or Bio::GFF::GFF2::Record::Value objects.

Returns: self

# File lib/bio/db/gff.rb, line 555
def replace_attributes(tag, *values)
  i = 0
  @attributes.reject! do |x|
    if x[0] == tag then
      if i >= values.size then
        true
      else
        x[1] = values[i]
        i += 1
        false
      end
    else
      false
    end
  end
  (i...(values.size)).each do |j|
    @attributes.push [ String.new(tag), values[j] ]
  end
  self
end

set_attribute(tag, value) click to toggle source

Sets value for the given tag. If the tag exists, the value of the tag is replaced with value. Note that if two or more tag-value pairs with the same name found, only the first tag-value pair is replaced.

If the tag does not exist, the tag-value pair is newly added.

Arguments:

(required) tag: String
(required) value: String or Bio::GFF::GFF2::Record::Value object.

Returns: value

# File lib/bio/db/gff.rb, line 532
def set_attribute(tag, value)
  ary = @attributes.find do |x|
    x[0] == tag
  end
  if ary then
    ary[1] = value
  else
    ary = [ String.new(tag), value ]
    @attributes.push ary
  end
  value
end

sort_attributes_by_tag!(tags = nil) { |x, y| ... } click to toggle source

Sorts attributes order by given tag name's order. If a block is given, the argument tags is ignored, and yields two tag names like Array#sort!.

Arguments:

(required or optional) tags: Array containing String objects

Returns: self

# File lib/bio/db/gff.rb, line 625
def sort_attributes_by_tag!(tags = nil)
  h = {}
  s = @attributes.size
  @attributes.each_with_index { |x, i|  h[x] = i }
  if block_given? then
    @attributes.sort! do |x, y|
      r = yield x[0], y[0]
      if r == 0 then
        r = (h[x] || s) <=> (h[y] || s)
      end
      r
    end
  else
    unless tags then
      raise ArgumentError, 'wrong number of arguments (0 for 1) or wrong argument value'
    end
    @attributes.sort! do |x, y|
      r = (tags.index(x[0]) || tags.size) <=> 
        (tags.index(y[0]) || tags.size)
      if r == 0 then
        r = (h[x] || s) <=> (h[y] || s)
      end
      r
    end
  end
  self
end

to_s() click to toggle source

Return the record as a GFF2 compatible string

# File lib/bio/db/gff.rb, line 455
def to_s
  cmnt = if defined?(@comment) and @comment and
             !@comment.to_s.strip.empty? then
           @comment.gsub(/[\r\n]+/, ' ')
         else
           false
         end
  return "\##{cmnt}\n" if self.comment_only? and cmnt
  [
   gff2_column_to_s(@seqname),
   gff2_column_to_s(@source),
   gff2_column_to_s(@feature),
   gff2_column_to_s(@start),
   gff2_column_to_s(@end),
   gff2_column_to_s(@score),
   gff2_column_to_s(@strand),
   gff2_column_to_s(@frame),
   attributes_to_s(@attributes)
  ].join("\t") + 
    (cmnt ? "\t\##{cmnt}\n" : "\n")
end