Class: Bio::Ipcress

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

Defined Under Namespace

Classes: PrimerSet, Result, Results

Class Method Summary collapse

Class Method Details

.parse(ipcress_output_string) ⇒ Object

A full Ipcress result looks something like this. Parse it into an array of Ipcress::Result objects

** Message: Loaded [1] experiments

Ipcress result


Experiment: AE12_pmid21856836_16S
   Primers: A B
    Target: gi|335929284|gb|JN048683.1|:filter(unmasked) Methanocella conradii HZ254 16S ribosomal RNA gene, partial sequence
   Matches: 19/20 14/15
   Product: 502 bp (range 2-10000)

Result type: forward

…AAACTTAAAGGAATTGGCGG.….….….….….…. # forward

||||| ||| |||||| |||-->

5'-AAACTYAAAKGAATTGRCGG-3' 3'-CRTGTGTGGCGGGCA-5' # primers

<--| |||||||||||||

.….….….….….….…..CGTGTGTGGCGGGCA… # revcomp – ipcress: gi|335929284|gb|JN048683.1|:filter(unmasked) AE12_pmid21856836_16S 502 A 826 1 B 1313 1 forward – completed ipcress analysis


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# File 'lib/bio/appl/ipcress.rb', line 27

def self.parse(ipcress_output_string)
  results = Results.new
  
  ipcress_output_string.split(/\nIpcress result\n--------------\n/m).each_with_index do |result_chunk, index|
    next if index == 0 # ignore the first chunk since that isn't a result
    
    lines = result_chunk.split("\n").collect{|l| l.strip}
    
    result = Result.new
    i=0
    result.experiment_name  = lines[i].match(/^Experiment: (.+)$/)[1]; i+=1
    result.primers     = lines[i].match(/^Primers: (.+)$/)[1]; i+=1
    result.target      = lines[i].match(/^Target: (.+)$/)[1]; i+=1
    result.matches     = lines[i].match(/^Matches: (.+)$/)[1]; i+=1
    result.product     = lines[i].match(/^Product: (.+)$/)[1]; i+=1
    result.result_type = lines[i].match(/^Result type: (.+)$/)[1]
    
    i+= 2
    result.forward_matching_sequence = lines[i].match(/^\.\.\.(\w+)\.+ \# forward$/)[1]
    i+= 2
    matching = lines[i].match(/^5'\-(\w+)-3' 3'\-(\w+)-5' \# primers$/)
    result.forward_primer_sequence = matching[1]
    result.reverse_primer_sequence = matching[2]
    i+= 2
    result.reverse_matching_sequence = lines[i].match(/^\.+(\w+)\.\.\. \# revcomp$/)[1]
    
    i+= 2
    matching = lines[i].match(/^ipcress: (\S+) (\S+) (\d+) [AB] (\d+) (\d+) [AB] (\d+) (\d+) (\S+)$/)
    result.length = matching[3].to_i
    result.start = matching[4].to_i
    result.forward_mismatches = matching[5].to_i
    result.reverse_mismatches = matching[7].to_i
    
    results.push result
  end
  return results
end

.run(primer_set, fasta_file, options = {}) ⇒ Object

Run ipcress

  • primer_set: a PrimerSet object with defined forward and reverse primers

  • fasta_file: a String path to a fasta file that will be used as template

  • options hash: contains less-used parameters

** :min_distance: the minimum length of product to be amplified (default 100) ** :max_distance: the maxmimum length of product to be amplified (default 1000) ** :ipcress_path: path the ipcress executable (default 'ipcress') ** :mismatches: number of mismatches allowable (-m parameter to ipcress binary, default 0)

Return an array of parsed Result objects


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# File 'lib/bio/appl/ipcress.rb', line 76

def self.run(primer_set, fasta_file, options={})
  raise unless primer_set.kind_of?(PrimerSet)
  raise unless fasta_file.kind_of?(String)
  options[:ipcress_path] ||= 'ipcress'
  
  Tempfile.open('ipcress') do |tempfile|
    # Write a tempfile that contains the primer set to be queried
    primers = primer_set.to_ipcress_format(options)
    tempfile.puts primers
    tempfile.close
    
    command = [
      options[:ipcress_path],
    ]
    if options[:mismatches]
      command.push '-m'
      command.push options[:mismatches].to_s
    end
    command.push tempfile.path
    command.push fasta_file

    Bio::Command.call_command_open3(command) do |stdin, stdout, stderr|
      out = stdout.read
      raise stderr.read if out == '' #if there is a problem running ipcress e.g. the fasta file isn't found
      
      return parse(out)
    end
  end
end