class FastaWriter

Fasta writer

Public Class Methods

new(fn) click to toggle source

Open a FASTA stream for writing

# File lib/bigbio/db/fasta/fastawriter.rb, line 6
def initialize fn
  @f = File.open(fn,"w")
end

Public Instance Methods

close() click to toggle source
# File lib/bigbio/db/fasta/fastawriter.rb, line 27
def close
  @f.close
end
write(id, seq = nil) click to toggle source

write a FASTA item. Normally write using id,seq. If only one item is passed in, the item should respond to descr and seq, or id and seq.

# File lib/bigbio/db/fasta/fastawriter.rb, line 12
def write id, seq = nil
  if seq == nil
    item = id
    if item.respond_to?(:descr)
      @f.write ">"+item.descr+"\n"
    else
      @f.write ">"+item.id+"\n"
    end
    @f.write item.seq.to_s.strip+"\n"
  else
    @f.write ">"+id+"\n"
    @f.write seq.to_s.strip+"\n"
  end
end