Class: Bio::TMHMM::TmHmmResult

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/tmhmm/tmhmm_runner.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Attribute Details

#domains ⇒ Object (readonly)

Returns the value of attribute domains.



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# File 'lib/bio/appl/tmhmm/tmhmm_runner.rb', line 28

def domains
  @domains
end

Class Method Details

.create_from_short_line(line) ⇒ Object

initialise with the output line of a eg. PFF0290w len=293 ExpAA=145.77 First60=20.51 PredHel=7 Topology=o39-61i101-120o140-162i169-186o196-218i230-252o262-284i



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# File 'lib/bio/appl/tmhmm/tmhmm_runner.rb', line 33

def self.create_from_short_line(line)
  protein = Bio::Transmembrane::OrientedTransmembraneDomainProtein.new
  
  splits = line.strip.split("\t")
  if splits.length != 6
    raise Exception, "Incorrectly parsed short line from TMHMM: #{line}"
  end
  
  substrate = splits[5]
  if substrate.gsub!(/^Topology\=[io]/,'').nil?
    raise Exception, "Badly parsed Topology hit: #{substrate}"
  end
  
  matches = substrate.match('^(\d+?)\-')
  if !matches
    return protein #no transmembrane domains predicted
  end
  
  # eat the string from the beginning adding the transmembrane domains
  prev = matches[1]
  substrate.gsub!(/^(\d+?)-/,'')
  # match all the middle bits
  reg = /^(\d+?)([io])(\d+?)\-/
  while matches =substrate.match(reg)
    tmd = Bio::Transmembrane::OrientedTransmembraneDomain.new
    tmd.start = prev.to_i
    tmd.stop = matches[1].to_i
    tmd.orientation = parse_orientation_from_last_location(matches[2])
    protein.push tmd
    
    prev = matches[3]
    substrate.gsub!(reg, '')
  end
  #match the last bit
  if !(matches = substrate.match('(\d+?)([io])$'))
    raise Exception, "Failed to parse the last bit of: #{substrate}"
  end
  tmd = Bio::Transmembrane::OrientedTransmembraneDomain.new
  tmd.start = prev.to_i
  tmd.stop = matches[1].to_i
  tmd.orientation = parse_orientation_from_last_location(matches[2])
  protein.push tmd
  
  return protein
end

.parse_orientation_from_last_location(last_location) ⇒ Object 



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# File 'lib/bio/appl/tmhmm/tmhmm_runner.rb', line 79

def self.parse_orientation_from_last_location(last_location)
  case last_location
    when 'i'  
    return Bio::Transmembrane::OrientedTransmembraneDomain::OUTSIDE_IN
    when 'o'
    return Bio::Transmembrane::OrientedTransmembraneDomain::INSIDE_OUT
  else
    raise Exception, "Badly parsed topology hit due to orientation character: #{substrate}"
  end
end