Module: RGFA::LinearPaths

Included in:
RGFA
Defined in:
lib/rgfa/linear_paths.rb

Overview

Methods for the RGFA class, which allow to find and merge linear paths.

Instance Method Summary collapse

Instance Method Details

#linear_path(s, exclude = Set.new) ⇒ Array<RGFA::SegmentEnd>

Find a path without branches.

The path must include segment and excludes segments in exclude. Any segment used in the returned path will be added to exclude

Parameters:

  • a segment name or instance

  • (defaults to: Set.new)

    a set of segment names to exclude from the path

Returns:



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# File 'lib/rgfa/linear_paths.rb', line 21

def linear_path(s, exclude = Set.new)
  s = s.to_sym
  cs = connectivity(s)
  segpath = RGFA::SegmentEndsPath.new()
  [:B, :E].each_with_index do |et, i|
    if cs[i] == 1
      exclude << s
      segpath.pop
      segpath += traverse_linear_path(RGFA::SegmentEnd.new([s, et]), exclude)
    end
  end
  return (segpath.size < 2) ? nil : segpath
end

#linear_paths ⇒ Array<Array<RGFA::SegmentEnd>>

Find all unbranched paths in the graph.

Returns:



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# File 'lib/rgfa/linear_paths.rb', line 38

def linear_paths
  exclude = Set.new
  retval = []
  segnames = segment_names
  progress_log_init(:linear_paths, "segments", segnames.size,
    "Detect linear paths (#{segnames.size} segments)")  if @progress
  segnames.each do |sn|
    progress_log(:linear_paths) if @progress
    next if exclude.include?(sn)
    retval << linear_path(sn, exclude)
  end
  progress_log_end(:linear_paths)
  return retval.compact
end

#merge_linear_path(segpath, **options) ⇒ RGFA

Merge a linear path, i.e. a path of segments without extra-branches Limitations: all containments und paths involving merged segments are deleted.

Parameters:

  • a linear path, such as that retrieved by #linear_path

  • optional keyword arguments

Options Hash (**options):

  • :merged_name (String, :short, nil) — default: nil —

    if nil, the merged_name is automatically computed; if :short, a name is computed starting with “merged1” and calling next until an available name is founf; if String, the name to use

  • :cut_counts (Boolean) — default: false —

    if true, total count in merged segment m, composed of segments s of set S is multiplied by the factor Sum(|s in S|)/|m|

Returns:

  • self

See Also:



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# File 'lib/rgfa/linear_paths.rb', line 72

def merge_linear_path(segpath, **options)
  return if segpath.size < 2
  segpath.map!{|se|se.to_segment_end}
  if segpath[1..-2].any? {|sn,et| connectivity(sn) != [1,1]}
    raise ArgumentError, "The specified path is not linear"
  end
  merged, first_reversed, last_reversed =
    create_merged_segment(segpath, options)
  self << merged
  link_merged(merged.name, segpath.first.to_segment_end.invert_end_type,
              first_reversed)
  link_merged(merged.name, segpath.last, last_reversed)
  segpath.each do |sn_et|
    delete_segment(sn_et.segment)
    progress_log(:merge_linear_paths, 0.05) if @progress
  end
  self
end

#merge_linear_paths(**options) ⇒ RGFA

Merge all linear paths in the graph, i.e. paths of segments without extra-branches Limitations: all containments und paths involving merged segments are deleted.

Parameters:

  • optional keyword arguments

Options Hash (**options):

  • :merged_name (String, :short, nil) — default: nil —

    if nil, the merged_name is automatically computed; if :short, a name is computed starting with “merged1” and calling next until an available name is founf; if String, the name to use

  • :cut_counts (Boolean) — default: false —

    if true, total count in merged segment m, composed of segments s of set S is multiplied by the factor Sum(|s in S|)/|m|

Returns:

  • self



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# File 'lib/rgfa/linear_paths.rb', line 97

def merge_linear_paths(**options)
  paths = linear_paths
  psize = paths.flatten.size / 2
  progress_log_init(:merge_linear_paths, "segments", psize,
    "Merge #{paths.size} linear paths (#{psize} segments)") if @progress
  paths.each do |path|
    merge_linear_path(path, **options)
  end
  progress_log_end(:merge_linear_paths)
  self
end