Module: PasvLib::Io

Defined in:
lib/pasv_lib/io.rb

Instance Method Summary collapse

Instance Method Details

#read_queries(fname) ⇒ Object 



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# File 'lib/pasv_lib/io.rb', line 27

def read_queries fname
  queries = {}

  ParseFasta::SeqFile.open(fname).each_record do |rec|
    if has_gaps? rec.seq
      raise PasvLib::ParseError,
            "Record '#{rec.header}' had gaps!  Did you accidentally " \
            "provide aligned sequences?"
    end

    header          = "pasv_query___#{rec.header}"
    queries[header] = rec.seq
  end

  queries
end

#read_refs(fname) ⇒ Object 



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# File 'lib/pasv_lib/io.rb', line 5

def read_refs fname
  refs = {}

  ParseFasta::SeqFile.open(fname).each_record do |rec|
    if has_gaps? rec.seq
      raise PasvLib::ParseError,
            "Record '#{rec.header}' had gaps!  Did you accidentally " \
            "provide aligned sequences?"
    end

    if refs.count.zero?
      head = "first_pasv_ref"
    else
      head = "pasv_ref___#{rec.id}"
    end

    refs[head] = rec.seq
  end

  refs
end