Class: FastaWriter

Inherits:
Object
  • Object
show all
Defined in:
lib/bigbio/db/fasta/fastawriter.rb

Overview

Fasta writer

Instance Method Summary collapse

Constructor Details

#initialize(fn) ⇒ FastaWriter

Open a FASTA stream for writing



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# File 'lib/bigbio/db/fasta/fastawriter.rb', line 6

def initialize fn
  @f = File.open(fn,"w")
end

Instance Method Details

#close ⇒ Object 



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# File 'lib/bigbio/db/fasta/fastawriter.rb', line 27

def close
  @f.close
end

#write(id, seq = nil) ⇒ Object

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.



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# 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