class Bio::TargetP::Report

A parser and container class for TargetP report.

Constants

DELIMITER

Delimiter

RS

Delimiter

Attributes

cleavage_site_prediction[R]

Returns 'included' or 'not included'. If the value is 'included', Bio::TargetP::Report#prediction['TPlen'] contains a valid value.

cutoff[R]

Returns a Hash of cutoff values.

networks[R]

Returns “PLANT'' or “NON-PLANT'' networks.

pred[R]

Returns a Hash of the prediction results.

{“Name”=>“MGI_2141503”, “Loc.”=>“_”, “RC”=>3, “SP”=>0.271,

"other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}

Keys: Name, Len, SP, mTP, other, Loc, RC Optional key for PLANT networks: cTP Optional key in Cleavage site: TPlen

Use 'Length' and 'Loc.' instead of 'Len' and 'Loc' respectively for the version 1.0 report.

prediction[R]

Returns a Hash of the prediction results.

{“Name”=>“MGI_2141503”, “Loc.”=>“_”, “RC”=>3, “SP”=>0.271,

"other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}

Keys: Name, Len, SP, mTP, other, Loc, RC Optional key for PLANT networks: cTP Optional key in Cleavage site: TPlen

Use 'Length' and 'Loc.' instead of 'Len' and 'Loc' respectively for the version 1.0 report.

query_sequences[R]

Returns the query sequences.

version[R]

Returns the program version.

Public Class Methods

new(str) click to toggle source

Sets output report.

   # File lib/bio/appl/targetp/report.rb
63 def initialize(str)
64   @version                  = nil
65   @query_sequences          = nil
66   @cleavage_site_prediction = nil
67   @networks                 = nil
68   @prediction               = {}
69   @cutoff                   = {}
70   parse_entry(str)
71 end

Public Instance Methods

entry_id()
Alias for: name
length()
Alias for: query_len
loc() click to toggle source

Returns the predicted localization signal:

  1. S (Signal peptide)

  2. M (mTP)

  3. C (cTP)

  4. *

  5. _

    # File lib/bio/appl/targetp/report.rb
 97 def loc
 98   if @prediction['Loc'] 
 99     @prediction['Loc']   # version 1.0
100   else
101     @prediction['Loc.']  # version 1.1
102   end
103 end
name() click to toggle source

Returns the name of query sequence.

   # File lib/bio/appl/targetp/report.rb
76 def name
77   @prediction['Name']
78 end
Also aliased as: entry_id
query_len() click to toggle source

Returns length of query sequence.

   # File lib/bio/appl/targetp/report.rb
82 def query_len
83   if @prediction['Len']
84     @prediction['Len']
85   else
86     @prediction['Length']
87   end
88 end
Also aliased as: length
rc() click to toggle source

Returns RC.

    # File lib/bio/appl/targetp/report.rb
106 def rc
107   @prediction['RC']
108 end

Private Instance Methods

parse_entry(str) click to toggle source
    # File lib/bio/appl/targetp/report.rb
113 def parse_entry(str)
114   labels = []
115   cutoff = []
116   values = []
117 
118   str.split("\n").each {|line|
119     case line
120     when /targetp v(\d+.\d+)/,/T A R G E T P\s+(\d+.\d+)/
121       @version = $1
122 
123     when /Number of (query|input) sequences:\s+(\d+)/
124       @query_sequences = $1.to_i
125 
126     when /Cleavage site predictions (\w.+)\./ 
127       @cleavage_site_prediction = $1
128 
129     when /Using (\w+.+) networks/
130       @networks = $1
131     when /Name +Len/
132       labels = line.sub(/^\#\s*/,'').split(/\s+/)
133 
134     when /cutoff/
135       cutoff = line.split(/\s+/)
136       cutoff.shift
137       labels[2, 4].each_with_index {|loc, i|
138         next if loc =~ /Loc/
139         @cutoff[loc] = cutoff[i].to_f
140       }
141     when /-----$/
142     when /^ +$/, ''
143     else
144       values = line.sub(/^\s*/,'').split(/\s+/)
145       values.each_with_index {|val, i|
146         label = labels[i]
147         case label
148         when 'RC', /Len/ 
149           val = val.to_i
150         when 'SP','mTP','cTP','other'
151           val = val.to_f
152         end
153         @prediction[label] = val
154       }
155     end
156   }
157 end