Class: Bio::GFF

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/gff.rb

Overview

DESCRIPTION

The Bio::GFF and Bio::GFF::Record classes describe data contained in a GFF-formatted file. For information on the GFF format, see http://www.sanger.ac.uk/Software/formats/GFF/. Data are represented in tab- delimited format, including

  • seqname
  • source
  • feature
  • start
  • end
  • score
  • strand
  • frame
  • attributes (optional)

For example: SEQ1 EMBL atg 103 105 . + 0 SEQ1 EMBL exon 103 172 . + 0 SEQ1 EMBL splice5 172 173 . + . SEQ1 netgene splice5 172 173 0.94 + . SEQ1 genie sp5-20 163 182 2.3 + . SEQ1 genie sp5-10 168 177 2.1 + . SEQ1 grail ATG 17 19 2.1 - 0

The Bio::GFF object is a container for Bio::GFF::Record objects, each representing a single line in the GFF file.

Direct Known Subclasses

GFF2, GFF3

Defined Under Namespace

Classes: GFF2, GFF3, Record

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str = '') ⇒ GFF

Creates a Bio::GFF object by building a collection of Bio::GFF::Record objects.

Create a Bio::GFF object the hard way this_gff = "SEQ1\tEMBL\tatg\t103\t105\t.\t+\t0\n" this_gff << "SEQ1\tEMBL\texon\t103\t172\t.\t+\t0\n" this_gff << "SEQ1\tEMBL\tsplice5\t172\t173\t.\t+\t.\n" this_gff << "SEQ1\tnetgene\tsplice5\t172\t173\t0.94\t+\t.\n" this_gff << "SEQ1\tgenie\tsp5-20\t163\t182\t2.3\t+\t.\n" this_gff << "SEQ1\tgenie\tsp5-10\t168\t177\t2.1\t+\t.\n" this_gff << "SEQ1\tgrail\tATG\t17\t19\t2.1\t-\t0\n" p Bio::GFF.new(this_gff)

or create one based on a GFF-formatted file: p Bio::GFF.new(File.open('my_data.gff')

Arguments:

  • str: string in GFF format
Returns

Bio::GFF object



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# File 'lib/bio/db/gff.rb', line 65

def initialize(str = '')
  @records = Array.new
  str.each_line do |line|
    @records << Record.new(line)
  end
end

Instance Attribute Details

#records ⇒ Object

An array of Bio::GFF::Record objects.



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# File 'lib/bio/db/gff.rb', line 73

def records
  @records
end