Class: Bio::GFF::GFF2::Record

Inherits:
Record show all
Includes:
Escape
Defined in:
lib/bio/db/gff.rb

Overview

Stores GFF2 record.

Direct Known Subclasses

Bio::GFF::GFF3::Record

Defined Under Namespace

Classes: Value

Constant Summary

Constants included from Escape

Escape::BACKSLASH, Escape::CHAR2BACKSLASH, Escape::CHAR2BACKSLASH_EXTENDED, Escape::IDENTIFIER_GFF2, Escape::NUMERIC_GFF2, Escape::PROHIBITED_GFF2_COLUMNS, Escape::PROHIBITED_GFF2_TAGS, Escape::UNSAFE_GFF2

Instance Attribute Summary collapse

Attributes inherited from Record

#attributes, #end, #feature, #frame, #score, #seqname, #source, #start, #strand

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(*arg) ⇒ Record

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)



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# File 'lib/bio/db/gff.rb', line 383

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

Instance Attribute Details

#comment ⇒ Object

Comment for the GFF record



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# File 'lib/bio/db/gff.rb', line 399

def comment
  @comment
end

Class Method Details

.parse(str) ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 362

def self.parse(str)
  self.new.parse(str)
end

Instance Method Details

#==(other) ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 480

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) ⇒ Object

Adds a new tag-value pair.

Arguments:

  • (required) tag: String

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

Returns

value



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# File 'lib/bio/db/gff.rb', line 584

def add_attribute(tag, value)
  @attributes.push([ String.new(tag), value ])
end

#attributes_to_hash ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 662

def attributes_to_hash
  h = {}
  @attributes.each do |x|
    key, val = x
    h[key] = val unless h[key]
  end
  h
end

#comment_only? ⇒ Boolean

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

Returns:

  • (Boolean) 


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# File 'lib/bio/db/gff.rb', line 440

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 ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 402

def comments
  warn "#{self.class.to_s}#comments is deprecated. Instead, use \"comment\"."
  self.comment
end

#comments=(str) ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 408

def comments=(str)
  warn "#{self.class.to_s}#comments= is deprecated. Instead, use \"comment=\"."
  self.comment = str
end

#delete_attribute(tag, value) ⇒ Object

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.



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# File 'lib/bio/db/gff.rb', line 598

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) ⇒ Object

Removes all attributes with the specified tag.

Arguments:

  • (required) tag: String

Returns

if removed, self. Otherwise, nil.



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# File 'lib/bio/db/gff.rb', line 613

def delete_attributes(tag)
  @attributes.reject! do |x|
    x[0] == tag
  end ? self : nil
end

#get_attribute(tag) ⇒ Object Also known as: attribute

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.



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# File 'lib/bio/db/gff.rb', line 502

def get_attribute(tag)
  ary = @attributes.assoc(tag)
  ary ? ary[1] : nil
end

#get_attributes(tag) ⇒ Object

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.



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# File 'lib/bio/db/gff.rb', line 515

def get_attributes(tag)
  ary = @attributes.find_all do |x|
    x[0] == tag
  end
  ary.collect! { |x| x[1] }
  ary
end

#parse(string) ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 415

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) ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 557

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) ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 534

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) ⇒ Object

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



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# File 'lib/bio/db/gff.rb', line 627

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 ⇒ Object

Return the record as a GFF2 compatible string



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# File 'lib/bio/db/gff.rb', line 457

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