Class: Bio::GFF::GFF3::FileIterator

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

Overview

GFF3::FileIterator takes a file and yields GFF3 records with their seek position included in the record.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename) ⇒ FileIterator

Returns a new instance of FileIterator.



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# File 'lib/bio/db/gff/file/gfffileiterator.rb', line 40

def initialize filename
  @fh = File.open(filename)
end

Instance Attribute Details

#fasta_io_seek ⇒ Object (readonly)

Returns the value of attribute fasta_io_seek.



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# File 'lib/bio/db/gff/file/gfffileiterator.rb', line 38

def fasta_io_seek
  @fasta_io_seek
end

#fh ⇒ Object

Returns the value of attribute fh.



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# File 'lib/bio/db/gff/file/gfffileiterator.rb', line 37

def fh
  @fh
end

Instance Method Details

#each_rec ⇒ Object

Iterate over every record in the file, yielding the seekpos and line containing the record



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# File 'lib/bio/db/gff/file/gfffileiterator.rb', line 46

def each_rec
  @fh.seek(0)
  fpos = 0
  @fh.each_line do | line |
    line = line.strip
    if line == "##FASTA"
      @fasta_io_seek = fpos
      break
    end
    if line.size != 0 and line !~ /^#/
      lastpos = @fh.tell
      yield fpos, line
      @fh.seek(lastpos) # reset filepos, just in case it changed
    end
    fpos = @fh.tell
  end
end

#each_sequence ⇒ Object

Iterate over all contained FASTA sequences, yielding the ID and sequence as a FASTA record. Normally call each_rec first and you can test for existing FASTA records if fasta_io_seek != nil



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# File 'lib/bio/db/gff/file/gfffileiterator.rb', line 67

def each_sequence
  if @fasta_io_seek == nil
    # Find the FASTA location first
    @fh.each_line do | line |
      break if line.strip == "##FASTA"
    end
  else
    @fh.seek(@fasta_io_seek)
  end
  fasta = Bio::GFF::FastaReader.new(@fh)
  fasta.each do | id, fastarec |
    yield id, fastarec
  end
end