Class: FastaFile

Inherits:
File
  • Object
show all
Defined in:
lib/parse_fasta/fasta_file.rb

Overview

Provides simple interface for parsing fasta format files. Gzipped files are no problem.

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.open(fname, *args) ⇒ FastaFile

Use it like IO::open

Parameters:

  • fname (String) —

    the name of the file to open

Returns:



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# File 'lib/parse_fasta/fasta_file.rb', line 30

def self.open(fname, *args)
  begin
    handle = Zlib::GzipReader.open(fname)
  rescue Zlib::GzipFile::Error => e
    handle = File.open(fname)
  end

  unless handle.each_char.peek[0] == '>'
    raise ParseFasta::DataFormatError
  end

  handle.close

  super
end

Instance Method Details

#each_record(separate_lines = nil) {|header, sequence| ... } ⇒ Object

Analagous to IO#each_line, #each_record is used to go through a fasta file record by record. It will accept gzipped files as well.

Examples:

Parsing a fasta file (default behavior, gzip files are fine)

FastaFile.open('reads.fna.gz').each_record do |header, sequence|
  puts [header, sequence.gc].join("\t")
end

Parsing a fasta file (with truthy value param)

FastaFile.open('reads.fna').each_record(1) do |header, sequence|
  # header => 'sequence_1'
  # sequence => ['AACTG', 'AGTCGT', ... ]
end

Parameters:

  • separate_lines (Object) (defaults to: nil) —

    If truthy, separate lines of record into an array of Sequences, but if falsy, yield a Sequence object for the sequence instead.

Yields:

  • The header and sequence for each record in the fasta file to the block

Yield Parameters:

  • header (String) —

    The header of the fasta record without the leading ‘>’

  • sequence (Sequence, Array<Sequence>) —

    The sequence of the fasta record. If ‘separate_lines` is falsy (the default behavior), will be Sequence, but if truthy will be Array<String>.

Raises:



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# File 'lib/parse_fasta/fasta_file.rb', line 95

def each_record(separate_lines=nil)
  begin
    f = Zlib::GzipReader.open(self)
  rescue Zlib::GzipFile::Error => e
    f = self
  end

  if separate_lines
    f.each("\n>") do |line|
      header, sequence = parse_line_separately(line)
      yield(header.strip, sequence)
    end

    # f.each_with_index(">") do |line, idx|
    #   if idx.zero?
    #     if line != ">"
    #       raise ParseFasta::DataFormatError
    #     end
    #   else
    #     header, sequence = parse_line_separately(line)
    #     yield(header.strip, sequence)
    #   end
    # end
  else
    f.each("\n>") do |line|
      header, sequence = parse_line(line)
      yield(header.strip, Sequence.new(sequence || ""))
    end

    # f.each_with_index(sep=/^>/) do |line, idx|
    #   if idx.zero?
    #     if line != ">"
    #       raise ParseFasta::DataFormatError
    #     end
    #   else
    #     header, sequence = parse_line(line)
    #     yield(header.strip, Sequence.new(sequence || ""))
    #   end
    # end
  end

  f.close if f.instance_of?(Zlib::GzipReader)
  return f
end

#each_record_fast {|header, sequence| ... } ⇒ Object

Note:

If the fastA file has spaces in the sequence, they will be retained. If this is a problem, use #each_record instead.

Fast version of #each_record

Yields the sequence as a String, not Sequence. No separate lines option.

Yields:

  • The header and sequence for each record in the fasta file to the block

Yield Parameters:

  • header (String) —

    The header of the fasta record without the leading ‘>’

  • sequence (String) —

    The sequence of the fasta record

Raises:



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# File 'lib/parse_fasta/fasta_file.rb', line 157

def each_record_fast
  begin
    f = Zlib::GzipReader.open(self)
  rescue Zlib::GzipFile::Error => e
    f = self
  end

  f.each("\n>") do |line|
    header, sequence = parse_line(line)

    raise ParseFasta::SequenceFormatError if sequence.include? ">"

    yield(header.strip, sequence)
  end

  f.close if f.instance_of?(Zlib::GzipReader)
  return f
end

#to_hash ⇒ Hash

Returns the records in the fasta file as a hash map with the headers as keys and the Sequences as values.

Examples:

Read a fastA into a hash table.

seqs = FastaFile.open('reads.fa').to_hash

Returns:

  • (Hash) —

    A hash with headers as keys, sequences as the values (Sequence objects)

Raises:



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# File 'lib/parse_fasta/fasta_file.rb', line 56

def to_hash
  hash = {}
  self.each_record do |head, seq|
    hash[head] = seq
  end

  hash
end