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



27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
 
# 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



76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
 
# 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