Class: RGFA

Inherits:
Object show all
Includes:
Comments, Connectivity, Containments, Headers, LinearPaths, Lines, Links, LoggerSupport, Multiplication, Paths, RGL, Segments, RGFATools
Defined in:
lib/rgfa.rb,
lib/rgfa.rb,
lib/rgfatools.rb

Overview

Main class of the RGFA library.

RGFA provides a representation of a GFA graph. It supports creating a graph from scratch, input and output from/to file or strings, as well as several operations on the graph. The examples below show how to create a RGFA object from scratch or from a GFA file, write the RGFA to file, output the string representation or a statistics report, and control the validation level.

Interacting with the graph

Examples:

Creating an empty RGFA object

gfa = RGFA.new

Parsing and writing GFA format

gfa = RGFA.from_file(filename) # parse GFA file
gfa.to_file(filename) # write to GFA file
puts gfa # show GFA representation of RGFA object

Basic statistics report

puts gfa.info # print report
puts gfa.info(short = true) # compact format, in one line

Validation

gfa = RGFA.from_file(filename, validate: 1) # default level is 2
gfa.validate = 3 # change validation level
gfa.turn_off_validations # equivalent to gfa.validate = 0
gfa.validate! # run post-validations (e.g. check segment names in links)

Defined Under Namespace

Modules: Comments, Connectivity, Containments, FieldParser, FieldValidator, FieldWriter, Headers, LinearPaths, Lines, Links, LoggerSupport, Multiplication, Paths, Segments, Sequence Classes: ByteArray, CIGAR, DuplicatedLabelError, Error, FieldArray, Line, LineMissingError, Logger, NumericArray, OrientedSegment, SegmentEnd, SegmentEndsPath, SegmentInfo

Constant Summary

Constants included from RGFATools::Multiplication

RGFATools::Multiplication::LINKS_DISTRIBUTION_POLICY

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from RGFATools::PBubbles

#remove_p_bubble, #remove_p_bubbles

Methods included from RGFATools::LinearPaths

#merge_linear_path

Methods included from RGFATools::SuperfluousLinks

#enforce_all_mandatory_links, #enforce_segment_mandatory_links, #remove_self_link, #remove_self_links

Methods included from RGFATools::Multiplication

#multiply_extended, #multiply_with_rgfatools

Methods included from RGFATools::InvertibleSegments

#randomly_orient_invertible, #randomly_orient_invertibles

Methods included from RGFATools::CopyNumber

#apply_copy_number, #apply_copy_numbers, #compute_copy_numbers, #delete_low_coverage_segments, #set_count_unit_length, #set_default_count_tag

Methods included from RGFATools::Artifacts

#remove_dead_ends, #remove_small_components

Methods included from LoggerSupport

#enable_progress_logging, #progress_log, #progress_log_end, #progress_log_init

Methods included from Multiplication

#multiply

Methods included from Connectivity

#connected_components, #connectivity, #cut_link?, #cut_segment?, #segment_connected_component, #split_connected_components

Methods included from LinearPaths

#linear_path, #linear_paths, #merge_linear_path, #merge_linear_paths

Methods included from Paths

#delete_path, #path, #path!, #paths, #paths_with

Methods included from Containments

#contained_in, #containing, #containment, #containment!, #containments, #containments_between, #delete_containment

Methods included from Links

#delete_link, #delete_other_links, #link, #link!, #link_from_to, #link_from_to!, #links, #links_between, #links_from, #links_from_to, #links_of, #links_to, #neighbours

Methods included from Segments

#connected_segments, #delete_segment, #segment, #segment!, #segments, #unconnect_segments

Methods included from Headers

#delete_headers, #header, #headers

Methods included from Lines

#<<, #rename, #rm

Methods included from Comments

#comments, #delete_comment, #delete_comments

Constructor Details

#initialize(validate: 2) ⇒ RGFA

Returns a new instance of RGFA.

Parameters:

  • validate (Integer) (defaults to: 2) —

    (defaults to: 2) the validation level; see “Validation level” under RGFA::Line#initialize.



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# File 'lib/rgfa.rb', line 107

def initialize(validate: 2)
  @validate = validate
  init_headers
  @segments = {}
  @links = []
  @containments = []
  @paths = {}
  @comments = []
  @segments_first_order = false
  @progress = false
  @default = {:count_tag => :RC, :unit_length => 1}
  @extensions_enabled = false
end

Instance Attribute Details

#validate ⇒ Object

Returns the value of attribute validate.



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# File 'lib/rgfa.rb', line 101

def validate
  @validate
end

Class Method Details

.from_file(filename, validate: 2) ⇒ RGFA

Creates a RGFA instance parsing the file with specified filename

Parameters:

  • filename (String)
  • validate (Integer) (defaults to: 2) —

    (defaults to: 2) the validation level; see “Validation level” under RGFA::Line#initialize.

Returns:

Raises:

  • if file cannot be opened for reading



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# File 'lib/rgfa.rb', line 207

def self.from_file(filename, validate: 2)
  gfa = RGFA.new(validate: validate)
  gfa.read_file(filename)
  return gfa
end

Instance Method Details

#==(other) ⇒ Boolean

Compare two RGFA instances.

Returns:

  • (Boolean) —

    are the lines of the two instances equivalent?



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# File 'lib/rgfa.rb', line 288

def ==(other)
  segments == other.segments and
    links == other.links and
    containments == other.containments and
    headers == other.headers and
    paths == other.paths
end

#clone ⇒ RGFA

Create a copy of the RGFA instance.

Returns:



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# File 'lib/rgfa.rb', line 175

def clone
  cpy = to_s.to_rgfa(validate: 0)
  cpy.validate = @validate
  cpy.enable_progress_logging if @progress
  cpy.require_segments_first_order if @segments_first_order
  return cpy
end

#disable_extensions ⇒ void

This method returns an undefined value.

Disable RGFATools extensions of RGFA methods



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# File 'lib/rgfatools.rb', line 98

def disable_extensions
  @extensions_enabled = false
end

#enable_extensions ⇒ void

This method returns an undefined value.

Enable RGFATools extensions of RGFA methods



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# File 'lib/rgfatools.rb', line 92

def enable_extensions
  @extensions_enabled = true
end

#info(short = false) ⇒ String

Output basic statistics about the graph’s sequence and topology information.

Compact output has the following keys:

  • ns: number of segments

  • nl: number of links

  • cc: number of connected components

  • de: number of dead ends

  • tl: total length of segment sequences

  • 50: N50 segment sequence length

Normal output outputs a table with the same information, plus some additional one: the length of the largest component, as well as the shortest and largest and 1st/2nd/3rd quartiles of segment sequence length.

Parameters:

  • short (boolean) (defaults to: false) —

    compact output as a single text line

Returns:

  • (String) —

    sequence and topology information collected from the graph.



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# File 'lib/rgfa.rb', line 242

def info(short = false)
  q, n50, tlen = lenstats
  nde = n_dead_ends()
  pde = "%.2f%%" % ((nde.to_f*100) / (segments.size*2))
  cc = connected_components()
  cc.map!{|c|c.map{|sn|segment!(sn).length!}.inject(:+)}
  if short
    return "ns=#{segments.size}\t"+
           "nl=#{links.size}\t"+
           "cc=#{cc.size}\t"+
           "de=#{nde}\t"+
           "tl=#{tlen}\t"+
           "50=#{n50}"
  end
  retval = []
  retval << "Segment count:               #{segments.size}"
  retval << "Links count:                 #{links.size}"
  retval << "Total length (bp):           #{tlen}"
  retval << "Dead ends:                   #{nde}"
  retval << "Percentage dead ends:        #{pde}"
  retval << "Connected components:        #{cc.size}"
  retval << "Largest component (bp):      #{cc.last}"
  retval << "N50 (bp):                    #{n50}"
  retval << "Shortest segment (bp):       #{q[0]}"
  retval << "Lower quartile segment (bp): #{q[1]}"
  retval << "Median segment (bp):         #{q[2]}"
  retval << "Upper quartile segment (bp): #{q[3]}"
  retval << "Longest segment (bp):        #{q[4]}"
  return retval
end

#n_dead_ends ⇒ Integer

Counts the dead ends.

Dead ends are here defined as segment ends without connections.

Returns:

  • (Integer) —

    number of dead ends in the graph



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# File 'lib/rgfa.rb', line 279

def n_dead_ends
  segments.inject(0) do |n,s|
    [:E, :B].each {|e| n+= 1 if links_of([s.name, e]).empty?}
    n
  end
end

#path_names ⇒ Array<Symbol>

List all names of path lines in the graph

Returns:



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# File 'lib/rgfa.rb', line 145

def path_names
  @paths.keys.compact
end

#read_file(filename) ⇒ self

Populates a RGFA instance reading from file with specified filename

Parameters:

Returns:

  • (self)

Raises:

  • if file cannot be opened for reading



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# File 'lib/rgfa.rb', line 187

def read_file(filename)
  if @progress
    linecount = `wc -l #{filename}`.strip.split(" ")[0].to_i
    progress_log_init(:read_file, "lines", linecount,
                      "Parse file with #{linecount} lines")
  end
  File.foreach(filename) do |line|
    self << line.chomp
    progress_log(:read_file) if @progress
  end
  progress_log_end(:read_file) if @progress
  validate! if @validate >= 1
  self
end

#require_segments_first_order ⇒ void

This method returns an undefined value.

Require that the links, containments and paths referring to a segment are added after the segment. Default: do not require any particular ordering.



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# File 'lib/rgfa.rb', line 126

def require_segments_first_order
  @segments_first_order = true
end

#segment_names ⇒ Array<Symbol>

List all names of segments in the graph

Returns:



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# File 'lib/rgfa.rb', line 139

def segment_names
  @segments.keys.compact
end

#to_file(filename) ⇒ void

This method returns an undefined value.

Write RGFA to file with specified filename; overwrites it if it exists

Parameters:

Raises:

  • if file cannot be opened for writing



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# File 'lib/rgfa.rb', line 218

def to_file(filename)
  File.open(filename, "w") {|f| each_line {|l| f.puts l}}
end

#to_rgfa ⇒ self

Return the gfa itself

Returns:

  • (self) 


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# File 'lib/rgfa.rb', line 169

def to_rgfa
  self
end

#to_s ⇒ String

Creates a string representation of RGFA conforming to the current specifications

Returns:



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# File 'lib/rgfa.rb', line 161

def to_s
  s = ""
  each_line {|line| s << line.to_s; s << "\n"}
  return s
end

#turn_off_validations ⇒ void

This method returns an undefined value.

Set the validation level to 0. See “Validation level” under RGFA::Line#initialize.



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# File 'lib/rgfa.rb', line 133

def turn_off_validations
  @validate = 0
end

#validate! ⇒ void

This method returns an undefined value.

Post-validation of the RGFA

Raises:

  • if validation fails



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# File 'lib/rgfa.rb', line 152

def validate!
  validate_segment_references!
  validate_path_links!
  return nil
end