class Bio::GFF::GFF2::Record

Stores GFF2 record.

Attributes

Comment for the GFF record

Public Class Methods

Source

    # File lib/bio/db/gff.rb
385 def initialize(*arg)
386   if arg.size == 1 then
387     parse(arg[0])
388   else
389     @seqname, @source, @feature,
390     start, endp, @score, @strand, frame,
391     @attributes = arg
392     @start = start ? start.to_i : nil
393     @end   = endp  ? endp.to_i : nil
394     @score = score ? score.to_f : nil
395     @frame = frame ? frame.to_i : nil
396   end
397   @attributes ||= []
398 end

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)

parse (str)

Source

    # File lib/bio/db/gff.rb
362 def self.parse(str)
363   ret = self.new
364   ret.parse(str)
365   ret
366 end

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

Public Instance Methods

== (other)

Source

    # File lib/bio/db/gff.rb
482 def ==(other)
483   super ||
484     ((self.class == other.class and
485       self.seqname == other.seqname and
486       self.source  == other.source and
487       self.feature == other.feature and
488       self.start   == other.start and
489       self.end     == other.end and
490       self.score   == other.score and
491       self.strand  == other.strand and
492       self.frame   == other.frame and
493       self.attributes == other.attributes) ? true : false)
494 end

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

Calls superclass method

add_attribute (tag, value)

Source

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

Adds a new tag-value pair.

Arguments:

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

Returns: value

attribute (tag)

Alias for: get_attribute

attributes_to_hash ()

Source

    # File lib/bio/db/gff.rb
664 def attributes_to_hash
665   h = {}
666   @attributes.each do |x|
667     key, val = x
668     h[key] = val unless h[key]
669   end
670   h
671 end

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

comment_only? ()

Source

    # File lib/bio/db/gff.rb
442 def comment_only?
443   if !@seqname and
444       !@source and
445       !@feature and
446       !@start and
447       !@end and
448       !@score and
449       !@strand and
450       !@frame and
451       @attributes.empty? then
452     true
453   else
454     false
455   end
456 end

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

comments ()

Source

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

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

comments= (str)

Source

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

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

delete_attribute (tag, value)

Source

    # File lib/bio/db/gff.rb
600 def delete_attribute(tag, value)
601   removed = nil
602   if i = @attributes.index([ tag, value ]) then
603     ary = @attributes.delete_at(i)
604     removed = ary[1]
605   end
606   removed
607 end

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.

delete_attributes (tag)

Source

    # File lib/bio/db/gff.rb
615 def delete_attributes(tag)
616   @attributes.reject! do |x|
617     x[0] == tag
618   end ? self : nil
619 end

Removes all attributes with the specified tag.

Arguments:

(required) tag: String

Returns: if removed, self. Otherwise, nil.

get_attribute (tag)

Source

    # File lib/bio/db/gff.rb
504 def get_attribute(tag)
505   ary = @attributes.assoc(tag)
506   ary ? ary[1] : nil
507 end

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.

Also aliased as: attribute

get_attributes (tag)

Source

    # File lib/bio/db/gff.rb
517 def get_attributes(tag)
518   ary = @attributes.find_all do |x|
519     x[0] == tag
520   end
521   ary.collect! { |x| x[1] }
522   ary
523 end

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.

parse (string)

Source

    # File lib/bio/db/gff.rb
417 def parse(string)
418   if /^\s*\#/ =~ string then
419     @comment = string[/\#(.*)/, 1].chomp
420     columns = []
421   else
422     columns = string.chomp.split("\t", 10)
423     @comment = columns[9][/\#(.*)/, 1].chomp if columns[9]
424   end
425 
426   @seqname, @source, @feature,
427   start, endp, score, @strand, frame =
428     columns[0, 8].collect { |x|
429     str = unescape(x)
430     str == '.' ? nil : str
431   }
432   @start = start ? start.to_i : nil
433   @end   = endp  ? endp.to_i : nil
434   @score = score ? score.to_f : nil
435   @frame = frame ? frame.to_i : nil
436 
437   @attributes = parse_attributes(columns[8])
438 end

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

replace_attributes (tag, *values)

Source

    # File lib/bio/db/gff.rb
559 def replace_attributes(tag, *values)
560   i = 0
561   @attributes.reject! do |x|
562     if x[0] == tag then
563       if i >= values.size then
564         true
565       else
566         x[1] = values[i]
567         i += 1
568         false
569       end
570     else
571       false
572     end
573   end
574   (i...(values.size)).each do |j|
575     @attributes.push [ String.new(tag), values[j] ]
576   end
577   self
578 end

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

set_attribute (tag, value)

Source

    # File lib/bio/db/gff.rb
536 def set_attribute(tag, value)
537   ary = @attributes.find do |x|
538     x[0] == tag
539   end
540   if ary then
541     ary[1] = value
542   else
543     ary = [ String.new(tag), value ]
544     @attributes.push ary
545   end
546   value
547 end

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

sort_attributes_by_tag! (tags = nil) { |x, y| ... }

Source

    # File lib/bio/db/gff.rb
629 def sort_attributes_by_tag!(tags = nil)
630   h = {}
631   s = @attributes.size
632   @attributes.each_with_index { |x, i|  h[x] = i }
633   if block_given? then
634     @attributes.sort! do |x, y|
635       r = yield x[0], y[0]
636       if r == 0 then
637         r = (h[x] || s) <=> (h[y] || s)
638       end
639       r
640     end
641   else
642     unless tags then
643       raise ArgumentError, 'wrong number of arguments (0 for 1) or wrong argument value'
644     end
645     @attributes.sort! do |x, y|
646       r = (tags.index(x[0]) || tags.size) <=> 
647         (tags.index(y[0]) || tags.size)
648       if r == 0 then
649         r = (h[x] || s) <=> (h[y] || s)
650       end
651       r
652     end
653   end
654   self
655 end

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

to_s ()

Source

    # File lib/bio/db/gff.rb
459 def to_s
460   cmnt = if defined?(@comment) and @comment and
461              !@comment.to_s.strip.empty? then
462            @comment.gsub(/[\r\n]+/, ' ')
463          else
464            false
465          end
466   return "\##{cmnt}\n" if self.comment_only? and cmnt
467   [
468    gff2_column_to_s(@seqname),
469    gff2_column_to_s(@source),
470    gff2_column_to_s(@feature),
471    gff2_column_to_s(@start),
472    gff2_column_to_s(@end),
473    gff2_column_to_s(@score),
474    gff2_column_to_s(@strand),
475    gff2_column_to_s(@frame),
476    attributes_to_s(@attributes)
477   ].join("\t") + 
478     (cmnt ? "\t\##{cmnt}\n" : "\n")
479 end

Return the record as a GFF2 compatible string