Module: Wrnap::Etl::Infernal

Defined in:
lib/wrnap/etl/infernal.rb

Constant Summary collapse

NAME_REGEX = 
/>>\s+(\S+)(.*\n){3}.*\s(\d+)\s+(\d+)\s+[\+-].*\n/
HIT_SEQUENCE = 
/^.*\d+\s+(.*)\s+\d+\s*$/
HIT_STRUCTURE = 
/([()<>{}\[\]\-_~,.:]+)\s+CS/
LOCAL_END = 
/\*\[\s*\d+\s*\]\*/

Class Method Summary collapse

Class Method Details

.convert_infernal_to_dot_bracket(structure) ⇒ Object 



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# File 'lib/wrnap/etl/infernal.rb', line 44

def convert_infernal_to_dot_bracket(structure)
  # http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html
  structure.gsub(/[_~,.:]/, ?.).gsub(/[(<{\[]/, ?().gsub(/[)>}\]]/, ?))
end

.load_all(file) ⇒ Object 



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# File 'lib/wrnap/etl/infernal.rb', line 10

def load_all(file)
  output = File.exist?(file) ? File.read(file) : file

  if output =~ /No hits detected that satisfy reporting thresholds/
    []
  else
    output.
      gsub(/^(.*\n)*Hit alignments:\n/, "").
      gsub(/Internal CM pipeline statistics summary:\n(.*\n)*$/, "").
      strip.split(?\n).reject(&:empty?).each_slice(10).map { |lines| parse_hit(lines.join(?\n)) }.compact
  end.wrnap
end

.parse_hit(output) ⇒ Object 



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# File 'lib/wrnap/etl/infernal.rb', line 23

def parse_hit(output)
  name = if (name_match = output.match(NAME_REGEX))
    # This is a pretty fancy regex, and there's no guarantee that the data has this info, so let's just test the waters here.
    _, id, _, seq_from, seq_to, _ = name_match.to_a
    "%s %d %d" % [id.split(?|).last, seq_from, seq_to]
  end

  unless (hit_sequence = pull_infernal_hit_sequence(output)) =~ LOCAL_END
    Stockholm.fit_structure_to_sequence(hit_sequence, pull_infernal_hit_structure(output)).tap { |rna| rna.comment = name if name }
  end
end

.pull_infernal_hit_sequence(output) ⇒ Object 



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# File 'lib/wrnap/etl/infernal.rb', line 35

def pull_infernal_hit_sequence(output)
  # Dots are gaps in Stockholm format, and this uses the Stockholm parser underneath.
  output.scan(HIT_SEQUENCE)[-1][-1].upcase.gsub(?-, ?.)
end

.pull_infernal_hit_structure(output) ⇒ Object 



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# File 'lib/wrnap/etl/infernal.rb', line 40

def pull_infernal_hit_structure(output)
  convert_infernal_to_dot_bracket(output.match(HIT_STRUCTURE)[1])
end