class Bio::GFF::GFF3

DESCRIPTION¶ ↑

Represents version 3 of GFF specification. For more information on version GFF3, see song.sourceforge.net/gff3.shtml

Constants

MetaData: stores GFF3 MetaData
VERSION

Attributes

gff_version[R]

GFF3 version string (String or nil). nil means “3”.

metadata[RW]

Metadata (except “##sequence-region”, “##gff-version”, “###”). Must be an array of Bio::GFF::GFF3::MetaData objects.

sequence_regions[RW]

Metadata of “##sequence-region”. Must be an array of Bio::GFF::GFF3::SequenceRegion objects.

sequences[RW]

Sequences bundled within GFF3. Must be an array of Bio::Sequence objects.

Public Class Methods

new(str = nil) click to toggle source

Creates a Bio::GFF::GFF3 object by building a collection of Bio::GFF::GFF3::Record (and metadata) objects.

Arguments:

str: string in GFF format

Returns: Bio::GFF object

    # File lib/bio/db/gff.rb
877 def initialize(str = nil)
878   @gff_version = nil
879   @records = []
880   @sequence_regions = []
881   @metadata = []
882   @sequences = []
883   @in_fasta = false
884   parse(str) if str
885 end

Public Instance Methods

parse(str) click to toggle source

Parses a GFF3 entries, and concatenated the parsed data.

Note that after “##FASTA” line is given, only fasta-formatted text is accepted.

Arguments:

str: string in GFF format

Returns: self

    # File lib/bio/db/gff.rb
911 def parse(str)
912   # if already after the ##FASTA line, parses fasta format and return
913   if @in_fasta then
914     parse_fasta(str)
915     return self
916   end
917 
918   if str.respond_to?(:gets) then
919     # str is a IO-like object
920     fst = nil
921   else
922     # str is a String
923     gff, sep, fst = str.split(/^(\>|##FASTA.*)/n, 2)
924     fst = sep + fst if sep == '>' and fst
925     str = gff
926   end
927 
928   # parses GFF lines
929   str.each_line do |line|
930     if /^\#\#([^\s]+)/ =~ line then
931       parse_metadata($1, line)
932       parse_fasta(str) if @in_fasta
933     elsif /^\>/ =~ line then
934       @in_fasta = true
935       parse_fasta(str, line)
936     else
937       @records << GFF3::Record.new(line)
938     end
939   end
940 
941   # parses fasta format when str is a String and fasta data exists
942   if fst then
943     @in_fasta = true
944     parse_fasta(fst)
945   end
946 
947   self
948 end

to_s() click to toggle source

string representation of whole entry.

    # File lib/bio/db/gff.rb
966 def to_s
967   ver = @gff_version || VERSION.to_s
968   if @sequences.size > 0 then
969     seqs = "##FASTA\n" +
970       @sequences.collect { |s| s.to_fasta(s.entry_id, 70) }.join('')
971   else
972     seqs = ''
973   end
974 
975   ([ "##gff-version #{escape(ver)}\n" ] +
976    @metadata.collect { |m| m.to_s } +
977    @sequence_regions.collect { |m| m.to_s } +
978    @records.collect{ |r| r.to_s }).join('') + seqs
979 end