Class: Bio::MAF::Access

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/maf/index.rb

Overview

Top-level class for working with a set of indexed MAF files. Provides a higher-level alternative to working with Parser and KyotoIndex objects directly.

Instantiate with Access.maf_dir and Access.file methods.

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(options) ⇒ Access

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Returns a new instance of Access.



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# File 'lib/bio/maf/index.rb', line 194

def initialize(options)
  @parse_options = options
  @indices = {}
  @maf_by_chrom = {}
  if options[:dir]
    scan_dir(options[:dir])
  elsif options[:maf]
    if options[:index]
      LOG.debug { "Opening index file #{options[:index]}" }
      index = KyotoIndex.open(options[:index])
      register_index(index,
                     options[:maf])
      index.close
    else
      idx_f = find_index_file(options[:maf])
      if idx_f
        index = KyotoIndex.open(idx_f)
        register_index(index, options[:maf])
        index.close
      end
    end
  else
    raise "Must specify :dir or :maf!"
  end
  if options[:maf] && @indices.empty?
    # MAF file explicitly given but no index
    # build a temporary one
    # (could build a real one, too...)
    maf = options[:maf]
    parser = Parser.new(maf, @parse_options)
    LOG.warn { "WARNING: building temporary index on #{maf}." }
    index = KyotoIndex.build(parser, '%')
    register_index(index, maf)
  end
end

Instance Attribute Details

#block_filter ⇒ Hash

Block filter to apply.

Returns:

  • (Hash)

See Also:



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# File 'lib/bio/maf/index.rb', line 83

def block_filter
  @block_filter
end

#indices ⇒ Object (readonly)

Returns the value of attribute indices.



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# File 'lib/bio/maf/index.rb', line 84

def indices
  @indices
end

#parse_options ⇒ Hash

Parser options.

Returns:

  • (Hash)

See Also:



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# File 'lib/bio/maf/index.rb', line 75

def parse_options
  @parse_options
end

#sequence_filter ⇒ Hash

Sequence filter to apply.

Returns:

  • (Hash)

See Also:



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# File 'lib/bio/maf/index.rb', line 79

def sequence_filter
  @sequence_filter
end

Class Method Details

.file(maf, index = nil, options = {}) ⇒ Access

Provides access to a single MAF file. If this file is not indexed, it will be fully parsed to create a temporary in-memory index. For large MAF files or ones which will be used multiple times, this is inefficient, and an index file should be created with maf_index(1).

Parameters:

  • maf (String) —

    path to MAF file

  • index (String) (defaults to: nil) —

    Kyoto Cabinet index file

  • options (Hash) (defaults to: {}) —

    parser options

Returns:



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# File 'lib/bio/maf/index.rb', line 108

def self.file(maf, index=nil, options={})
  o = options.dup
  o[:maf] = maf
  o[:index] = index if index
  self.new(o)
end

.maf_dir(dir, options = {}) ⇒ Access

Provides access to a directory of indexed MAF files. Any files with .maf suffixes and accompanying .kct indexes in the given directory will be accessible.

Parameters:

  • dir (String) —

    directory to scan

  • options (Hash) (defaults to: {}) —

    parser options

Returns:



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# File 'lib/bio/maf/index.rb', line 92

def self.maf_dir(dir, options={})
  o = options.dup
  o[:dir] = dir
  self.new(o)
end

Instance Method Details

#chrom_index(chrom) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



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# File 'lib/bio/maf/index.rb', line 264

def chrom_index(chrom)
  unless @indices.has_key? chrom
    raise "No index available for chromosome #{chrom}!"
  end
  index = @indices[chrom]
  if index.is_a? KyotoIndex
    # temporary
    index
  else
    KyotoIndex.open(index)
  end
end

#close ⇒ Object

Close all open resources, in particular Kyoto Cabinet database handles.



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# File 'lib/bio/maf/index.rb', line 117

def close
  @indices.values.each { |ki| ki.close }
end

#find(intervals) {|block| ... } ⇒ Array<Block>

Find all alignment blocks in the genomic regions in the list of Bio::GenomicInterval objects, and parse them with the given parser.

Parameters:

Yields:

  • (block) —

    each Block matched, in turn

Returns:

  • (Array<Block>) —

    each matching Block, if no block given

See Also:



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# File 'lib/bio/maf/index.rb', line 131

def find(intervals, &blk)
  if block_given?
    by_chrom = intervals.group_by { |i| i.chrom }
    by_chrom.keys.each do |chrom|
      unless @indices.has_key? chrom
        raise "No index available for chromosome #{chrom}!"
      end
    end
    by_chrom.each do |chrom, c_intervals|
      with_index(chrom) do |index|
        with_parser(chrom) do |parser|
          index.find(c_intervals, parser, block_filter, &blk)
        end
      end
    end
  else
    acc = []
    self.find(intervals) { |block| acc << block }
    acc
  end
end

#find_index_file(maf) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



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# File 'lib/bio/maf/index.rb', line 231

def find_index_file(maf)
  dir = File.dirname(maf)
  base = File.basename(maf)
  noext = base.gsub(/\.maf.*/, '')
  idx = [base, noext].collect { |n| "#{dir}/#{n}.kct" }.find { |path| File.exist? path }
end

#register_index(index, maf) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



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# File 'lib/bio/maf/index.rb', line 239

def register_index(index, maf)
  unless index.maf_file == File.basename(maf)
    raise "Index #{index.path} was created for #{index.maf_file}, not #{File.basename(maf)}!"
  end
  if index.path.to_s.start_with? '%'
    @indices[index.ref_seq] = index
  else
    @indices[index.ref_seq] = index.path.to_s
  end
  @maf_by_chrom[index.ref_seq] = maf
end

#scan_dir(dir) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



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# File 'lib/bio/maf/index.rb', line 252

def scan_dir(dir)
  Dir.glob("#{dir}/*.kct").each do |index_f|
    index = KyotoIndex.open(index_f)
    maf = "#{dir}/#{index.maf_file}"
    if File.exist? maf
      register_index(index, maf)
    end
    index.close
  end
end

#slice(interval) {|block| ... } ⇒ Array<Block>

Find and parse all alignment blocks in the genomic region given by a Bio::GenomicInterval, and truncate them to just the region intersecting that interval.

Parameters:

Yields:

  • (block) —

    each Block matched, in turn

Returns:

  • (Array<Block>) —

    each matching Block, if no block given

See Also:



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# File 'lib/bio/maf/index.rb', line 182

def slice(interval, &blk)
  with_index(interval.chrom) do |index|
    with_parser(interval.chrom) do |parser|
      s = index.slice(interval, parser, block_filter, &blk)
      block_given? ? s : s.to_a
    end
  end
end

#tile(interval) {|tiler| ... } ⇒ Object

Find and parse all alignment blocks in the genomic region given by a Bio::GenomicInterval, and combine them to synthesize a single alignment covering that interval exactly.

Parameters:

Yields:

  • (tiler) —

    a Tiler ready to operate on the given interval



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# File 'lib/bio/maf/index.rb', line 161

def tile(interval)
  with_index(interval.chrom) do |index|
    with_parser(interval.chrom) do |parser|
      tiler = Tiler.new
      tiler.index = index
      tiler.parser = parser
      tiler.interval = interval
      yield tiler
    end
  end
end

#with_index(chrom) ⇒ Object 



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# File 'lib/bio/maf/index.rb', line 277

def with_index(chrom)
  index = chrom_index(chrom)
  LOG.debug { "Selected index #{index} for sequence #{chrom}." }
  begin
    yield index
  ensure
    index.close unless index.path.to_s.start_with? '%'
  end
end

#with_parser(chrom) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



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# File 'lib/bio/maf/index.rb', line 288

def with_parser(chrom)
  LOG.debug { "Creating parser with options #{@parse_options.inspect}" }
  parser = Parser.new(@maf_by_chrom[chrom], @parse_options)
  parser.sequence_filter = self.sequence_filter
  begin
    yield parser
  ensure
    parser.close
  end
end