Module: GenomerPluginSummary::Enumerators

Included in:
Contigs, Metrics, Sequences
Defined in:
lib/genomer-plugin-summary/enumerators.rb

Instance Method Summary collapse

Instance Method Details

#enumerator_for(type, scaffold) ⇒ Object 



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# File 'lib/genomer-plugin-summary/enumerators.rb', line 5

def enumerator_for(type,scaffold)
  send('enumerator_for_' + type.to_s, scaffold)
end

#enumerator_for_all(scaffold) ⇒ Object 



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# File 'lib/genomer-plugin-summary/enumerators.rb', line 67

def enumerator_for_all(scaffold)
  scaffold.inject([0,[]]) do |memo,entry|
    position, entries = memo

    i = {:sequence   => entry.sequence,
         :start      => position + 1,
         :stop       => position + entry.sequence.length,
         :type       => entry.entry_type,
         :id         => entry.entry_type == :sequence ? entry.source : nil}

    [position + entry.sequence.length, entries << i]
  end.last
end

#enumerator_for_contig(scaffold) ⇒ Object 



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# File 'lib/genomer-plugin-summary/enumerators.rb', line 19

def enumerator_for_contig(scaffold)
  genome = scaffold.mapping(&:sequence).to_a.join
  regions = genome.
    gsub(/([^Nn])([Nn])/,'\1 \2').
    gsub(/([Nn])([^Nn])/,'\1 \2').
    scan(/[^\s]+/)

  regions.inject([0,1,[]]) do |memo,entry|
    position, number, entries = memo

    if entry.downcase.include? 'n'
      next [position + entry.length, number, entries]
    end

    i = {:sequence => entry,
         :start    => position + 1,
         :stop     => position + entry.length,
         :type     => :contig,
         :id       => number}

    [position + entry.length, number + 1, entries << i]
  end.last
end

#enumerator_for_gap(scaffold) ⇒ Object 



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# File 'lib/genomer-plugin-summary/enumerators.rb', line 43

def enumerator_for_gap(scaffold)
  genome = scaffold.mapping(&:sequence).to_a.join
  regions = genome.
    gsub(/([^Nn])([Nn])/,'\1 \2').
    gsub(/([Nn])([^Nn])/,'\1 \2').
    scan(/[^\s]+/)

  regions.inject([0,1,[]]) do |memo,entry|
    position, number, entries = memo

    unless entry.downcase.include? 'n'
      next [position + entry.length, number, entries]
    end

    i = {:sequence => entry,
         :start    => position + 1,
         :stop     => position + entry.length,
         :type     => :gap,
         :id       => number}

    [position + entry.length, number + 1, entries << i]
  end.last
end

#enumerator_for_sequence(scaffold) ⇒ Object 



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# File 'lib/genomer-plugin-summary/enumerators.rb', line 9

def enumerator_for_sequence(scaffold)
  enumerator_for_all(scaffold).
    selecting{|i| i[:type] == :sequence}
end

#enumerator_for_unresolved(scaffold) ⇒ Object 



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# File 'lib/genomer-plugin-summary/enumerators.rb', line 14

def enumerator_for_unresolved(scaffold)
  enumerator_for_all(scaffold).
    selecting{|i| i[:type] == :unresolved}
end